SMTL ID : 5lu7.1

Heptose isomerase GmhA mutant - D61A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.64, E.68, H.183 Chain D: Q.175 Ligands: M7P.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.64, A:E.68, A:H.183 ZN.5: 5 residues within 4Å: Chain A: Q.175 Chain D: H.64, E.68, H.183 Ligands: M7P.2 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.64, D:E.68, D:H.183 ZN.6: 5 residues within 4Å: Chain B: H.64, E.68, H.183 Chain C: Q.175 Ligands: M7P.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.64, B:E.68, B:H.183, H2O.6, H2O.12 ZN.8: 5 residues within 4Å: Chain B: Q.175 Chain C: H.64, E.68, H.183 Ligands: M7P.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.64, C:E.68, C:H.183, H2O.12

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

M7P.2: 16 residues within 4Å: Chain A: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain B: A.94, N.97, D.98 Chain D: E.68, R.72, F.73 Ligands: ZN.5 16 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A, 3 interactions with chain D Hydrogen bonds: B:N.97, B:D.98, A:N.55, A:G.57, A:S.58, A:S.123, A:T.124, A:T.124, A:S.125, A:S.128, A:Q.175, D:S.71, D:F.73 Water bridges: A:N.55, A:N.55, D:R.72 M7P.7: 18 residues within 4Å: Chain A: A.94, N.97, D.98 Chain B: N.55, G.56, G.57, S.58, S.123, T.124, S.125, S.128, T.171, Q.175 Chain C: E.68, S.71, R.72, F.73 Ligands: ZN.8 16 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:N.55, B:G.57, B:S.58, B:S.123, B:T.124, B:S.125, B:S.128, B:Q.175, C:S.71, C:F.73, A:N.97, A:D.98 Water bridges: B:N.55, B:N.55, B:Q.175, B:Q.175 M7P.9: 17 residues within 4Å: Chain B: E.68, S.71, R.72, F.73 Chain C: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain D: A.94, N.97, D.98 Ligands: ZN.6 19 PLIP interactions: 3 interactions with chain B, 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:S.71, B:F.73, C:N.55, C:G.57, C:S.58, C:S.123, C:S.123, C:T.124, C:S.125, C:S.128, C:Q.175, D:N.97, D:D.98 Water bridges: B:R.72, C:N.55, C:T.124, C:T.124, C:Q.175, C:Q.175 M7P.13: 17 residues within 4Å: Chain A: E.68, R.72, F.73 Chain C: A.94, N.97, D.98 Chain D: N.55, G.56, G.57, S.58, S.123, T.124, S.125, S.128, T.171, Q.175 Ligands: ZN.1 16 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:N.55, D:G.57, D:S.58, D:S.123, D:T.124, D:S.125, D:S.128, D:Q.175, C:N.97, C:D.98, A:S.71, A:F.73 Water bridges: D:N.55, D:N.55, D:T.171, D:T.171

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

PG4.3: 6 residues within 4Å: Chain A: R.28, A.31, T.32, K.35, D.161, L.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:R.34 PG4.4: 4 residues within 4Å: Chain A: I.44, A.45, G.47, I.193 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.47 PG4.10: 5 residues within 4Å: Chain C: R.28, A.31, T.32, K.35, L.162 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.35

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 1 residues within 4Å: Chain C: I.44 No protein-ligand interaction detected (PLIP) EDO.12: 1 residues within 4Å: Chain C: R.157 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vivoli, M. et al., A half-site multimeric enzyme achieves its cooperativity without conformational changes. Sci Rep (2017)

Release Date

2017-12-06

Peptides

Phosphoheptose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Phosphoheptose isomerase