SMTL ID : 7cjp.1

Crystal structure of metal-free state of glucose isomerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

46 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: H.230, G.231, Q.234 Chain B: V.151, L.155, L.192, L.193, P.194, H.198 Ligand excluded by PLIP EDO.2: 13 residues within 4Å: Chain A: P.97, V.98, F.99, K.100, D.101, A.106, D.108, V.111 Chain B: R.334, A.365, A.366, R.368, M.370 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: R.23, D.28, A.29 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.76, L.79, D.80, E.128, L.129 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: D.295, F.296, D.297 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: D.353, S.355, A.356, F.360 Chain B: R.109, D.110, R.113 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: E.8, D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: W.16, H.54, D.56, D.57, N.92, F.94, T.95 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: K.159, R.205 Chain B: W.237, A.238 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: D.150, R.152 Chain B: D.273, L.274, S.277, R.321 Ligands: EDO.12, EDO.13 Ligand excluded by PLIP EDO.12: 12 residues within 4Å: Chain A: G.146, G.147, K.149, D.150, V.151 Chain B: W.270, D.273, R.321, L.330, L.335 Ligands: EDO.11, EDO.13 Ligand excluded by PLIP EDO.13: 12 residues within 4Å: Chain A: G.146, K.149, D.150, V.151, R.152 Chain B: P.229, H.230, A.233, W.270, L.274 Ligands: EDO.11, EDO.12 Ligand excluded by PLIP EDO.14: 12 residues within 4Å: Chain A: R.334, A.365, A.366, R.368, M.370 Chain B: P.97, V.98, F.99, K.100, D.101, D.108, V.111 Ligand excluded by PLIP EDO.15: 12 residues within 4Å: Chain A: N.227, P.229, H.230, A.233, W.270, L.274 Chain B: G.146, K.149, D.150, V.151, R.152 Ligands: EDO.20 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: W.237, A.238 Chain B: D.156, K.159, R.205 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: G.19, W.20, Q.21, G.22, R.23, A.29 Ligand excluded by PLIP EDO.19: 10 residues within 4Å: Chain B: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, M.158, F.162 Ligand excluded by PLIP EDO.20: 11 residues within 4Å: Chain A: W.270, R.321, L.330, L.335 Chain B: G.146, G.147, A.148, K.149, D.150, V.151 Ligands: EDO.15 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: R.109, D.110, R.113 Chain B: D.353, S.355, A.356, F.360 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.23: 11 residues within 4Å: Chain B: T.30, R.31, R.292, T.293, E.294, D.295 Chain C: K.100 Chain D: A.366, A.367, R.368, G.369 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain C: H.230, G.231, Q.234 Chain D: V.151, L.155, L.192, L.193, P.194, H.198 Ligand excluded by PLIP EDO.25: 13 residues within 4Å: Chain C: P.97, V.98, F.99, K.100, D.101, A.106, D.108, V.111 Chain D: R.334, A.365, A.366, R.368, M.370 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: R.23, D.28, A.29 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: R.76, L.79, D.80, E.128, L.129 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain C: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: D.295, F.296, D.297 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain C: D.353, S.355, A.356, F.360 Chain D: R.109, D.110, R.113 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain C: E.8, D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: W.16, H.54, D.56, D.57, N.92, F.94, T.95 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: K.159, R.205 Chain D: W.237, A.238 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain C: D.150, R.152 Chain D: D.273, L.274, S.277, R.321 Ligands: EDO.35, EDO.36 Ligand excluded by PLIP EDO.35: 12 residues within 4Å: Chain C: G.146, G.147, K.149, D.150, V.151 Chain D: W.270, D.273, R.321, L.330, L.335 Ligands: EDO.34, EDO.36 Ligand excluded by PLIP EDO.36: 12 residues within 4Å: Chain C: G.146, K.149, D.150, V.151, R.152 Chain D: P.229, H.230, A.233, W.270, L.274 Ligands: EDO.34, EDO.35 Ligand excluded by PLIP EDO.37: 12 residues within 4Å: Chain C: R.334, A.365, A.366, R.368, M.370 Chain D: P.97, V.98, F.99, K.100, D.101, D.108, V.111 Ligand excluded by PLIP EDO.38: 12 residues within 4Å: Chain C: N.227, P.229, H.230, A.233, W.270, L.274 Chain D: G.146, K.149, D.150, V.151, R.152 Ligands: EDO.43 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain C: W.237, A.238 Chain D: D.156, K.159, R.205 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain D: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: G.19, W.20, Q.21, G.22, R.23, A.29 Ligand excluded by PLIP EDO.42: 10 residues within 4Å: Chain D: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, M.158, F.162 Ligand excluded by PLIP EDO.43: 11 residues within 4Å: Chain C: W.270, R.321, L.330, L.335 Chain D: G.146, G.147, A.148, K.149, D.150, V.151 Ligands: EDO.38 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain C: R.109, D.110, R.113 Chain D: D.353, S.355, A.356, F.360 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.46: 11 residues within 4Å: Chain A: K.100 Chain B: A.366, A.367, R.368, G.369 Chain D: T.30, R.31, R.292, T.293, E.294, D.295 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, K.H., Crystal structure of the metal-free state of glucose isomerase reveals its minimal open configuration for metal binding. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-07-14

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Xylose isomerase

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