SMTL ID : 2glk.1

High-resolution study of D-Xylose isomerase, 0.94A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.94 Å

Oligo State

homo-tetramer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.12 MN.2: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: GOL.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.5 MN.7: 5 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.28 MN.8: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: GOL.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.21 MN.13: 5 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.44 MN.14: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: GOL.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.38 MN.19: 5 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.61 MN.20: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: GOL.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.54

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.2 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: D.9, R.10, E.276, R.284, Y.310, K.314 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: W.20, D.24, P.25, Y.254, D.255, Q.256 Chain C: P.25 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: P.229, H.230, A.233 Chain D: G.146, K.149, D.150, V.151 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.8 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: D.9, R.10, E.276, R.284, Y.310, K.314 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: W.20, D.24, P.25, Y.254, D.255, Q.256 Chain D: P.25 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: P.229, H.230, A.233 Chain C: G.146, K.149, D.150, V.151 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain C: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.14 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain C: D.9, R.10, E.276, R.284, Y.310, K.314 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: P.25 Chain C: W.20, D.24, P.25, Y.254, D.255, Q.256 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: G.146, K.149, D.150, V.151 Chain C: P.229, H.230, A.233 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain D: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.20 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain D: D.9, R.10, E.276, R.284, Y.310, K.314 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: P.25 Chain D: W.20, D.24, P.25, Y.254, D.255, Q.256 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: G.146, K.149, D.150, V.151 Chain D: P.229, H.230, A.233 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katz, A.K. et al., Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-05-16

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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