SMTL ID : 3u3h.1

X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

homo-tetramer

Ligands

4 x 03W: (2R)-propane-1,1,2,3-tetrol(Non-covalent)

03W.1: 14 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: FMT.2, MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.16, A:H.54, A:E.181, A:D.245 Water bridges: A:N.215, A:K.289 Salt bridges: A:H.220 03W.6: 14 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: FMT.7, MG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.16, B:H.54, B:E.181, B:D.245 Water bridges: B:N.215, B:K.289 Salt bridges: B:H.220 03W.11: 14 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: FMT.12, MG.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:W.16, C:H.54, C:E.181, C:D.245, C:D.287 Water bridges: C:N.215, C:K.289 Salt bridges: C:H.220 03W.16: 14 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: FMT.17, MG.18 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:W.16, D:H.54, D:E.181, D:D.245, D:D.287 Water bridges: D:N.215, D:K.289 Salt bridges: D:H.220

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 11 residues within 4Å: Chain A: W.137, E.181, K.183, E.217, H.220, D.255, D.287 Chain C: F.26 Ligands: 03W.1, MG.3, MG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.183, A:H.220 FMT.7: 11 residues within 4Å: Chain B: W.137, E.181, K.183, E.217, H.220, D.255, D.287 Chain D: F.26 Ligands: 03W.6, MG.8, MG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.183, B:H.220 FMT.12: 11 residues within 4Å: Chain A: F.26 Chain C: W.137, E.181, K.183, E.217, H.220, D.255, D.287 Ligands: 03W.11, MG.13, MG.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.183, C:H.220 FMT.17: 11 residues within 4Å: Chain B: F.26 Chain D: W.137, E.181, K.183, E.217, H.220, D.255, D.287 Ligands: 03W.16, MG.18, MG.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.183, D:H.220

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: 03W.1, FMT.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.4: 7 residues within 4Å: Chain A: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: FMT.2 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.18 MG.8: 7 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: 03W.6, FMT.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.9: 7 residues within 4Å: Chain B: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: FMT.7 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.38 MG.13: 7 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: 03W.11, FMT.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.14: 7 residues within 4Å: Chain C: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: FMT.12 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.59 MG.18: 7 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: 03W.16, FMT.17 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 MG.19: 7 residues within 4Å: Chain D: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: FMT.17 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.79

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 11 residues within 4Å: Chain A: W.16, W.20, H.54, D.57, N.92, F.94, T.95, K.289 Chain C: P.25, F.26, G.27 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.16, A:F.94 Water bridges: A:N.92 MRD.10: 11 residues within 4Å: Chain B: W.16, W.20, H.54, D.57, N.92, F.94, T.95, K.289 Chain D: P.25, F.26, G.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.16, B:F.94 Water bridges: B:N.92 MRD.15: 11 residues within 4Å: Chain A: P.25, F.26, G.27 Chain C: W.16, W.20, H.54, D.57, N.92, F.94, T.95, K.289 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.16, C:F.94 Water bridges: C:N.92 MRD.20: 11 residues within 4Å: Chain B: P.25, F.26, G.27 Chain D: W.16, W.20, H.54, D.57, N.92, F.94, T.95, K.289 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.16, D:F.94 Water bridges: D:N.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toteva, M.M. et al., Binding Energy and Catalysis by d-Xylose Isomerase: Kinetic, Product, and X-ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde. Biochemistry (2011)

Release Date

2011-10-26

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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