SMTL ID : 1gw9.1

Tri-iodide derivative of Xylose Isomerase from Streptomyces Rubiginosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: LXC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 CA.2: 5 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.220, A:D.255, A:D.257, H2O.10, H2O.10 CA.34: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: LXC.37 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 CA.35: 5 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.220, B:D.255, B:D.257, H2O.23, H2O.23 CA.67: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: LXC.70 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 CA.68: 5 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.220, C:D.255, C:D.257, H2O.37, H2O.37 CA.100: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: LXC.103 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 CA.101: 5 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.220, D:D.255, D:D.257, H2O.50, H2O.50

8 x LXC: beta-L-xylopyranose(Non-covalent)

LXC.3: 6 residues within 4Å: Chain A: D.295 Chain D: A.332, R.334, R.368, G.369, A.371 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:A.332, D:G.369, A:D.295, A:D.295 Salt bridges: D:R.334 Water bridges: A:D.297 LXC.4: 11 residues within 4Å: Chain A: H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.54, A:E.181, A:H.220 Water bridges: A:N.215, A:N.215 Salt bridges: A:H.54, A:K.289 LXC.36: 6 residues within 4Å: Chain B: D.295 Chain C: A.332, R.334, R.368, G.369, A.371 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.332, C:G.369, B:D.295 Salt bridges: C:R.334 LXC.37: 11 residues within 4Å: Chain B: H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: CA.34 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.54, B:T.90, B:E.181, B:H.220 Water bridges: B:N.215, B:N.215 Salt bridges: B:H.54, B:K.289 LXC.69: 6 residues within 4Å: Chain B: A.332, R.334, R.368, G.369, A.371 Chain C: D.295 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.332, B:G.369, C:D.295 Salt bridges: B:R.334 LXC.70: 11 residues within 4Å: Chain A: F.26 Chain C: H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: CA.67 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.54, C:T.90, C:E.181, C:H.220 Water bridges: C:N.215, C:N.215 Salt bridges: C:H.54, C:K.289 LXC.102: 6 residues within 4Å: Chain A: A.332, R.334, R.368, G.369, A.371 Chain D: D.295 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:A.332, A:G.369, D:D.295, D:D.295 Salt bridges: A:R.334 Water bridges: D:D.297 LXC.103: 11 residues within 4Å: Chain B: F.26 Chain D: H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: CA.100 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.54, D:E.181, D:H.220 Water bridges: D:N.215, D:N.215 Salt bridges: D:H.54, D:K.289

116 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 3 residues within 4Å: Chain A: T.12, H.49 Ligands: IOD.6 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: R.10, P.283 Ligands: IOD.5, IOD.7 Ligand excluded by PLIP IOD.7: 5 residues within 4Å: Chain A: R.10, S.281, P.283 Ligands: IOD.6, IOD.8 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: E.132, P.283 Ligands: IOD.7 Ligand excluded by PLIP IOD.9: 6 residues within 4Å: Chain A: Q.234, W.237, A.238 Chain B: A.201, F.202 Ligands: IOD.10 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: A.238 Chain B: R.205 Ligands: IOD.9, IOD.11 Ligand excluded by PLIP IOD.11: 6 residues within 4Å: Chain A: L.200, I.203, E.204, K.240 Ligands: IOD.10, IOD.12 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: E.204, P.209, K.240 Ligands: IOD.11, IOD.13 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: E.204, P.209, E.210, K.240 Ligands: IOD.12 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: F.104, G.138, M.158, F.162 Ligands: IOD.15, IOD.18 Ligand excluded by PLIP IOD.15: 6 residues within 4Å: Chain A: F.104, A.136, G.138 Ligands: IOD.14, IOD.16, IOD.18 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain A: T.91, L.93, A.136, W.137 Ligands: IOD.15 Ligand excluded by PLIP IOD.17: 5 residues within 4Å: Chain A: F.104, T.119, Y.134, A.136, L.165 Ligand excluded by PLIP IOD.18: 6 residues within 4Å: Chain A: L.93, G.103, F.104, E.141 Ligands: IOD.14, IOD.15 Ligand excluded by PLIP IOD.19: 5 residues within 4Å: Chain A: D.24, P.25 Chain C: E.186, P.187 Ligands: IOD.20 Ligand excluded by PLIP IOD.20: 7 residues within 4Å: Chain A: P.25, E.186, Y.254 Chain C: P.25, E.186 Ligands: IOD.19, IOD.86 Ligand excluded by PLIP IOD.21: 4 residues within 4Å: Chain A: L.236, G.239, K.240, L.241 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: H.382, G.385 Ligands: IOD.23 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain A: D.381, H.382, A.386 Ligands: IOD.22 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain A: F.94 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: Q.41 Ligands: IOD.26, IOD.33 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: E.38, Q.41 Ligands: IOD.25 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: L.193, P.194 Chain B: Q.234 Ligand excluded by PLIP IOD.28: 5 residues within 4Å: Chain A: G.138, E.141, M.158, I.191, L.192 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: N.250, G.263 Chain D: R.266 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: E.70, H.71, R.74 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: N.227 Chain B: G.146 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: R.316, A.319 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: R.42 Ligands: IOD.25 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain B: T.12, H.49 Ligands: IOD.39 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain B: R.10, P.283 Ligands: IOD.38, IOD.40 Ligand excluded by PLIP IOD.40: 5 residues within 4Å: Chain B: R.10, S.281, P.283 Ligands: IOD.39, IOD.41 Ligand excluded by PLIP IOD.41: 3 residues within 4Å: Chain B: E.132, P.283 Ligands: IOD.40 Ligand excluded by PLIP IOD.42: 6 residues within 4Å: Chain A: A.201, F.202 Chain B: Q.234, W.237, A.238 Ligands: IOD.43 Ligand excluded by PLIP IOD.43: 4 residues within 4Å: Chain A: R.205 Chain B: A.238 Ligands: IOD.42, IOD.44 Ligand excluded by PLIP IOD.44: 6 residues within 4Å: Chain B: L.200, I.203, E.204, K.240 Ligands: IOD.43, IOD.45 Ligand excluded by PLIP IOD.45: 5 residues within 4Å: Chain B: E.204, P.209, K.240 Ligands: IOD.44, IOD.46 Ligand excluded by PLIP IOD.46: 5 residues within 4Å: Chain B: E.204, P.209, E.210, K.240 Ligands: IOD.45 Ligand excluded by PLIP IOD.47: 6 residues within 4Å: Chain B: F.104, G.138, M.158, F.162 Ligands: IOD.48, IOD.51 Ligand excluded by PLIP IOD.48: 6 residues within 4Å: Chain B: F.104, A.136, G.138 Ligands: IOD.47, IOD.49, IOD.51 Ligand excluded by PLIP IOD.49: 5 residues within 4Å: Chain B: T.91, L.93, A.136, W.137 Ligands: IOD.48 Ligand excluded by PLIP IOD.50: 5 residues within 4Å: Chain B: F.104, T.119, Y.134, A.136, L.165 Ligand excluded by PLIP IOD.51: 6 residues within 4Å: Chain B: L.93, G.103, F.104, E.141 Ligands: IOD.47, IOD.48 Ligand excluded by PLIP IOD.52: 5 residues within 4Å: Chain B: D.24, P.25 Chain D: E.186, P.187 Ligands: IOD.53 Ligand excluded by PLIP IOD.53: 7 residues within 4Å: Chain B: P.25, E.186, Y.254 Chain D: P.25, E.186 Ligands: IOD.52, IOD.119 Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain B: L.236, G.239, K.240, L.241 Ligand excluded by PLIP IOD.55: 3 residues within 4Å: Chain B: H.382, G.385 Ligands: IOD.56 Ligand excluded by PLIP IOD.56: 4 residues within 4Å: Chain B: D.381, H.382, A.386 Ligands: IOD.55 Ligand excluded by PLIP IOD.57: 1 residues within 4Å: Chain B: F.94 Ligand excluded by PLIP IOD.58: 3 residues within 4Å: Chain B: Q.41 Ligands: IOD.59, IOD.66 Ligand excluded by PLIP IOD.59: 3 residues within 4Å: Chain B: E.38, Q.41 Ligands: IOD.58 Ligand excluded by PLIP IOD.60: 3 residues within 4Å: Chain A: Q.234 Chain B: L.193, P.194 Ligand excluded by PLIP IOD.61: 5 residues within 4Å: Chain B: G.138, E.141, M.158, I.191, L.192 Ligand excluded by PLIP IOD.62: 3 residues within 4Å: Chain B: N.250, G.263 Chain C: R.266 Ligand excluded by PLIP IOD.63: 3 residues within 4Å: Chain B: E.70, H.71, R.74 Ligand excluded by PLIP IOD.64: 2 residues within 4Å: Chain A: G.146 Chain B: N.227 Ligand excluded by PLIP IOD.65: 2 residues within 4Å: Chain B: R.316, A.319 Ligand excluded by PLIP IOD.66: 2 residues within 4Å: Chain B: R.42 Ligands: IOD.58 Ligand excluded by PLIP IOD.71: 3 residues within 4Å: Chain C: T.12, H.49 Ligands: IOD.72 Ligand excluded by PLIP IOD.72: 4 residues within 4Å: Chain C: R.10, P.283 Ligands: IOD.71, IOD.73 Ligand excluded by PLIP IOD.73: 5 residues within 4Å: Chain C: R.10, S.281, P.283 Ligands: IOD.72, IOD.74 Ligand excluded by PLIP IOD.74: 3 residues within 4Å: Chain C: E.132, P.283 Ligands: IOD.73 Ligand excluded by PLIP IOD.75: 6 residues within 4Å: Chain C: Q.234, W.237, A.238 Chain D: A.201, F.202 Ligands: IOD.76 Ligand excluded by PLIP IOD.76: 4 residues within 4Å: Chain C: A.238 Chain D: R.205 Ligands: IOD.75, IOD.77 Ligand excluded by PLIP IOD.77: 6 residues within 4Å: Chain C: L.200, I.203, E.204, K.240 Ligands: IOD.76, IOD.78 Ligand excluded by PLIP IOD.78: 5 residues within 4Å: Chain C: E.204, P.209, K.240 Ligands: IOD.77, IOD.79 Ligand excluded by PLIP IOD.79: 5 residues within 4Å: Chain C: E.204, P.209, E.210, K.240 Ligands: IOD.78 Ligand excluded by PLIP IOD.80: 6 residues within 4Å: Chain C: F.104, G.138, M.158, F.162 Ligands: IOD.81, IOD.84 Ligand excluded by PLIP IOD.81: 6 residues within 4Å: Chain C: F.104, A.136, G.138 Ligands: IOD.80, IOD.82, IOD.84 Ligand excluded by PLIP IOD.82: 5 residues within 4Å: Chain C: T.91, L.93, A.136, W.137 Ligands: IOD.81 Ligand excluded by PLIP IOD.83: 5 residues within 4Å: Chain C: F.104, T.119, Y.134, A.136, L.165 Ligand excluded by PLIP IOD.84: 6 residues within 4Å: Chain C: L.93, G.103, F.104, E.141 Ligands: IOD.80, IOD.81 Ligand excluded by PLIP IOD.85: 5 residues within 4Å: Chain A: E.186, P.187 Chain C: D.24, P.25 Ligands: IOD.86 Ligand excluded by PLIP IOD.86: 7 residues within 4Å: Chain A: P.25, E.186 Chain C: P.25, E.186, Y.254 Ligands: IOD.20, IOD.85 Ligand excluded by PLIP IOD.87: 4 residues within 4Å: Chain C: L.236, G.239, K.240, L.241 Ligand excluded by PLIP IOD.88: 3 residues within 4Å: Chain C: H.382, G.385 Ligands: IOD.89 Ligand excluded by PLIP IOD.89: 4 residues within 4Å: Chain C: D.381, H.382, A.386 Ligands: IOD.88 Ligand excluded by PLIP IOD.90: 1 residues within 4Å: Chain C: F.94 Ligand excluded by PLIP IOD.91: 3 residues within 4Å: Chain C: Q.41 Ligands: IOD.92, IOD.99 Ligand excluded by PLIP IOD.92: 3 residues within 4Å: Chain C: E.38, Q.41 Ligands: IOD.91 Ligand excluded by PLIP IOD.93: 3 residues within 4Å: Chain C: L.193, P.194 Chain D: Q.234 Ligand excluded by PLIP IOD.94: 5 residues within 4Å: Chain C: G.138, E.141, M.158, I.191, L.192 Ligand excluded by PLIP IOD.95: 3 residues within 4Å: Chain B: R.266 Chain C: N.250, G.263 Ligand excluded by PLIP IOD.96: 3 residues within 4Å: Chain C: E.70, H.71, R.74 Ligand excluded by PLIP IOD.97: 2 residues within 4Å: Chain C: N.227 Chain D: G.146 Ligand excluded by PLIP IOD.98: 2 residues within 4Å: Chain C: R.316, A.319 Ligand excluded by PLIP IOD.99: 2 residues within 4Å: Chain C: R.42 Ligands: IOD.91 Ligand excluded by PLIP IOD.104: 3 residues within 4Å: Chain D: T.12, H.49 Ligands: IOD.105 Ligand excluded by PLIP IOD.105: 4 residues within 4Å: Chain D: R.10, P.283 Ligands: IOD.104, IOD.106 Ligand excluded by PLIP IOD.106: 5 residues within 4Å: Chain D: R.10, S.281, P.283 Ligands: IOD.105, IOD.107 Ligand excluded by PLIP IOD.107: 3 residues within 4Å: Chain D: E.132, P.283 Ligands: IOD.106 Ligand excluded by PLIP IOD.108: 6 residues within 4Å: Chain C: A.201, F.202 Chain D: Q.234, W.237, A.238 Ligands: IOD.109 Ligand excluded by PLIP IOD.109: 4 residues within 4Å: Chain C: R.205 Chain D: A.238 Ligands: IOD.108, IOD.110 Ligand excluded by PLIP IOD.110: 6 residues within 4Å: Chain D: L.200, I.203, E.204, K.240 Ligands: IOD.109, IOD.111 Ligand excluded by PLIP IOD.111: 5 residues within 4Å: Chain D: E.204, P.209, K.240 Ligands: IOD.110, IOD.112 Ligand excluded by PLIP IOD.112: 5 residues within 4Å: Chain D: E.204, P.209, E.210, K.240 Ligands: IOD.111 Ligand excluded by PLIP IOD.113: 6 residues within 4Å: Chain D: F.104, G.138, M.158, F.162 Ligands: IOD.114, IOD.117 Ligand excluded by PLIP IOD.114: 6 residues within 4Å: Chain D: F.104, A.136, G.138 Ligands: IOD.113, IOD.115, IOD.117 Ligand excluded by PLIP IOD.115: 5 residues within 4Å: Chain D: T.91, L.93, A.136, W.137 Ligands: IOD.114 Ligand excluded by PLIP IOD.116: 5 residues within 4Å: Chain D: F.104, T.119, Y.134, A.136, L.165 Ligand excluded by PLIP IOD.117: 6 residues within 4Å: Chain D: L.93, G.103, F.104, E.141 Ligands: IOD.113, IOD.114 Ligand excluded by PLIP IOD.118: 5 residues within 4Å: Chain B: E.186, P.187 Chain D: D.24, P.25 Ligands: IOD.119 Ligand excluded by PLIP IOD.119: 7 residues within 4Å: Chain B: P.25, E.186 Chain D: P.25, E.186, Y.254 Ligands: IOD.53, IOD.118 Ligand excluded by PLIP IOD.120: 4 residues within 4Å: Chain D: L.236, G.239, K.240, L.241 Ligand excluded by PLIP IOD.121: 3 residues within 4Å: Chain D: H.382, G.385 Ligands: IOD.122 Ligand excluded by PLIP IOD.122: 4 residues within 4Å: Chain D: D.381, H.382, A.386 Ligands: IOD.121 Ligand excluded by PLIP IOD.123: 1 residues within 4Å: Chain D: F.94 Ligand excluded by PLIP IOD.124: 3 residues within 4Å: Chain D: Q.41 Ligands: IOD.125, IOD.132 Ligand excluded by PLIP IOD.125: 3 residues within 4Å: Chain D: E.38, Q.41 Ligands: IOD.124 Ligand excluded by PLIP IOD.126: 3 residues within 4Å: Chain C: Q.234 Chain D: L.193, P.194 Ligand excluded by PLIP IOD.127: 5 residues within 4Å: Chain D: G.138, E.141, M.158, I.191, L.192 Ligand excluded by PLIP IOD.128: 3 residues within 4Å: Chain A: R.266 Chain D: N.250, G.263 Ligand excluded by PLIP IOD.129: 3 residues within 4Å: Chain D: E.70, H.71, R.74 Ligand excluded by PLIP IOD.130: 2 residues within 4Å: Chain C: G.146 Chain D: N.227 Ligand excluded by PLIP IOD.131: 2 residues within 4Å: Chain D: R.316, A.319 Ligand excluded by PLIP IOD.132: 2 residues within 4Å: Chain D: R.42 Ligands: IOD.124 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, G. et al., Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-06-06

Peptides

XYLOSE ISOMERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

XYLOSE ISOMERASE

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