SMTL ID : 8v2t.1

Phosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut148591

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x XLR: 1,5,6-trideoxy-6,6-difluoro-1-(N-hydroxyformamido)-6-phosphono-D-ribo-hexitol(Non-covalent)

XLR.1: 19 residues within 4Å: Chain A: N.77, G.78, G.79, S.80, S.145, T.146, S.147, S.150, T.193, P.194, Q.197 Chain B: H.86, E.90, F.95, H.205 Chain D: A.116, N.119, D.120 Ligands: ZN.6 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.77, A:G.79, A:S.80, A:S.80, A:S.145, A:T.146, A:T.146, A:S.147, A:S.147, A:S.150, A:Q.197, A:Q.197, D:N.119, D:D.120 Water bridges: A:N.77, A:S.80 XLR.5: 19 residues within 4Å: Chain A: H.86, E.90, F.95, H.205 Chain B: N.77, G.78, G.79, S.80, S.145, T.146, S.147, S.150, T.193, P.194, Q.197 Chain C: A.116, N.119, D.120 Ligands: ZN.2 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.77, B:G.79, B:S.80, B:S.80, B:S.145, B:T.146, B:T.146, B:S.147, B:S.147, B:S.150, B:Q.197, B:Q.197, C:N.119, C:D.120 Water bridges: B:N.77, B:S.80 XLR.9: 19 residues within 4Å: Chain B: A.116, N.119, D.120 Chain C: N.77, G.78, G.79, S.80, S.145, T.146, S.147, S.150, T.193, P.194, Q.197 Chain D: H.86, E.90, F.95, H.205 Ligands: ZN.14 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.77, C:G.79, C:S.80, C:S.80, C:S.145, C:T.146, C:T.146, C:S.147, C:S.147, C:S.150, C:Q.197, C:Q.197, B:N.119, B:D.120 Water bridges: C:N.77, C:S.80, B:D.120 XLR.13: 19 residues within 4Å: Chain A: A.116, N.119, D.120 Chain C: H.86, E.90, F.95, H.205 Chain D: N.77, G.78, G.79, S.80, S.145, T.146, S.147, S.150, T.193, P.194, Q.197 Ligands: ZN.10 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.77, D:G.79, D:S.80, D:S.80, D:S.145, D:T.146, D:T.146, D:S.147, D:S.147, D:S.150, D:Q.197, D:Q.197, A:N.119, A:D.120 Water bridges: D:N.77, D:S.80, A:D.120

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: H.86, E.90, F.95, H.205 Chain B: G.79, P.194, Q.197 Ligands: XLR.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:E.90, A:H.205 ZN.6: 8 residues within 4Å: Chain A: G.79, P.194, Q.197 Chain B: H.86, E.90, F.95, H.205 Ligands: XLR.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.86, B:E.90, B:H.205 ZN.10: 8 residues within 4Å: Chain C: H.86, E.90, F.95, H.205 Chain D: G.79, P.194, Q.197 Ligands: XLR.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.86, C:E.90, C:H.205 ZN.14: 8 residues within 4Å: Chain C: G.79, P.194, Q.197 Chain D: H.86, E.90, F.95, H.205 Ligands: XLR.9 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.86, D:E.90, D:H.205

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

CL.3: 5 residues within 4Å: Chain A: K.71, N.136 Chain C: K.71, N.136 Ligands: CL.11 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: K.71, N.136 Chain D: K.71, N.136 Ligands: CL.15 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: K.71, N.136 Chain C: K.71, N.136 Ligands: CL.3 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: K.71, N.136 Chain D: K.71, N.136 Ligands: CL.7 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: G.135, N.136, K.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.136, A:K.163 NA.8: 3 residues within 4Å: Chain B: G.135, N.136, K.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.135, B:K.163 NA.12: 3 residues within 4Å: Chain C: G.135, N.136, K.163 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.163 NA.16: 3 residues within 4Å: Chain D: G.135, N.136, K.163 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.135, D:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moreau, F. et al., Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria. J.Med.Chem. (2024)

Release Date

2023-12-06

Peptides

Phosphoheptose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Phosphoheptose isomerase

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