SMTL ID : 2xbl.1

Crystal structure of GmhA from Burkholderia pseudomallei in complex with product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.65, E.69, H.184 Chain D: Q.176 Ligands: M7P.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.65, A:E.69, A:E.69, A:H.184 ZN.4: 5 residues within 4Å: Chain B: H.65, E.69, H.184 Chain C: Q.176 Ligands: M7P.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.65, B:E.69, B:E.69, B:H.184 ZN.6: 5 residues within 4Å: Chain B: Q.176 Chain C: H.65, E.69, H.184 Ligands: M7P.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.65, C:E.69, C:E.69, C:H.184 ZN.9: 5 residues within 4Å: Chain A: Q.176 Chain D: H.65, E.69, H.184 Ligands: M7P.2 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.65, D:E.69, D:E.69, D:H.184

4 x M7P: 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose(Non-covalent)

M7P.2: 17 residues within 4Å: Chain A: N.56, G.57, G.58, S.59, S.124, T.125, S.126, S.129, T.172, Q.176 Chain B: A.95, N.98, D.99 Chain D: E.69, S.72, R.73 Ligands: ZN.9 16 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:N.98, A:N.56, A:G.58, A:S.59, A:S.124, A:T.125, A:S.126, A:S.129, D:S.72, D:F.74 Water bridges: B:D.99, A:N.56, A:N.56, A:T.172, A:T.172, A:Q.176 M7P.5: 18 residues within 4Å: Chain A: A.95, N.98, D.99 Chain B: N.56, G.57, G.58, S.59, S.124, T.125, S.126, S.129, T.172, Q.176 Chain C: E.69, S.72, R.73, F.74 Ligands: ZN.6 16 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:N.98, B:N.56, B:G.58, B:S.59, B:S.124, B:T.125, B:S.126, B:S.129, B:Q.176, C:S.72, C:F.74 Water bridges: A:D.99, B:N.56, B:N.56, B:S.126, B:S.126 M7P.7: 18 residues within 4Å: Chain B: E.69, S.72, R.73, F.74 Chain C: N.56, G.57, G.58, S.59, S.124, T.125, S.126, S.129, T.172, Q.176 Chain D: A.95, N.98, D.99 Ligands: ZN.4 19 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: C:N.56, C:G.58, C:S.59, C:S.124, C:T.125, C:S.126, C:S.129, D:N.98, D:D.99, B:S.72, B:R.73, B:F.74 Water bridges: C:N.56, C:N.56, C:T.125, C:T.125, C:S.126, C:S.126, C:Q.176 M7P.10: 18 residues within 4Å: Chain A: E.69, S.72, R.73, F.74 Chain C: A.95, N.98, D.99 Chain D: N.56, G.57, G.58, S.59, S.124, T.125, S.126, S.129, T.172, Q.176 Ligands: ZN.1 16 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D, 3 interactions with chain A Hydrogen bonds: C:N.98, C:D.99, D:N.56, D:G.58, D:S.59, D:S.124, D:T.125, D:S.126, D:S.129, D:Q.176, A:S.72, A:R.73, A:F.74 Water bridges: D:N.56, D:N.56, D:T.172

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: R.29, A.32, T.33, K.36, L.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.36 Water bridges: A:T.33

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 5 residues within 4Å: Chain C: R.29, A.32, T.33, K.36, L.163 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.36

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain D: A.32, T.33, K.36, L.163 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harmer, N.J., The Structure of Sedoheptulose-7-Phosphate Isomerase from Burkholderia Pseudomallei Reveals a Zinc Binding Site at the Heart of the Active Site. J.Mol.Biol. (2010)

Release Date

2010-05-19

Peptides

PHOSPHOHEPTOSE ISOMERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PHOSPHOHEPTOSE ISOMERASE