SMTL ID : 3n4a.1

Crystal structure of D-Xylose Isomerase in complex with S-1,2-Propandiol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, A:H.219, A:D.254, A:D.256, H2O.14 MN.2: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: PGO.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286, H2O.6 MN.5: 5 residues within 4Å: Chain B: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, B:H.219, B:D.254, B:D.256, H2O.27 MN.6: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: PGO.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286, H2O.19 MN.9: 5 residues within 4Å: Chain C: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.216, C:H.219, C:D.254, C:D.256, H2O.41 MN.10: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: PGO.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286, H2O.33 MN.13: 5 residues within 4Å: Chain D: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.216, D:H.219, D:D.254, D:D.256, H2O.54 MN.14: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: PGO.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286, H2O.46

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: A.200, F.201 Chain D: Q.233, W.236, A.237 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: A.200, F.201 Chain C: Q.233, W.236, A.237 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: Q.233, W.236, A.237 Chain C: A.200, F.201 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: Q.233, W.236, A.237 Chain D: A.200, F.201 Ligand excluded by PLIP

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 8 residues within 4Å: Chain A: W.15, H.53, F.93, W.136, E.180, D.244, D.286 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.180 Water bridges: A:T.89, A:T.90, A:N.214 PGO.8: 8 residues within 4Å: Chain B: W.15, H.53, F.93, W.136, E.180, D.244, D.286 Ligands: MN.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.180 Water bridges: B:T.89, B:T.90, B:N.214 PGO.12: 8 residues within 4Å: Chain C: W.15, H.53, F.93, W.136, E.180, D.244, D.286 Ligands: MN.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.180 Water bridges: C:T.89, C:T.90, C:N.214 PGO.16: 8 residues within 4Å: Chain D: W.15, H.53, F.93, W.136, E.180, D.244, D.286 Ligands: MN.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.180 Water bridges: D:T.89, D:T.90, D:D.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Behnen, J. et al., Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Chemmedchem (2012)

Release Date

2011-05-25

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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