SMTL ID : 5ltz.1

GmhA_mutant Q175E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-tetramer

Ligands

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

PG4.1: 5 residues within 4Å: Chain A: R.28, A.31, T.32, K.35, L.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.35 PG4.6: 4 residues within 4Å: Chain B: Q.110 Chain D: I.44, G.79 Ligands: NA.15 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.47

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.64, E.68, H.183 Chain D: E.175 Ligands: I22.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.64, A:E.68, A:H.183, D:E.175 ZN.4: 5 residues within 4Å: Chain A: E.175 Chain D: H.64, E.68, H.183 Ligands: I22.3 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.64, D:E.68, D:H.183, A:E.175 ZN.8: 5 residues within 4Å: Chain B: H.64, E.68, H.183 Chain C: E.175 Ligands: I22.11 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.64, B:E.68, B:H.183, C:E.175 ZN.10: 5 residues within 4Å: Chain B: E.175 Chain C: H.64, E.68, H.183 Ligands: I22.9 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Metal complexes: B:E.175, C:H.64, C:E.68, C:H.183

4 x I22: D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE(Non-covalent)

I22.3: 16 residues within 4Å: Chain A: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, E.175 Chain B: N.97, D.98 Chain D: H.64, E.68, R.72, F.73 Ligands: ZN.4 15 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:N.55, A:G.57, A:S.58, A:S.123, A:T.124, A:S.125, A:S.128, D:F.73, B:N.97, B:D.98 Water bridges: A:N.55, A:N.55, A:S.58, A:S.58, A:T.171 I22.5: 17 residues within 4Å: Chain A: H.64, E.68, H.183 Chain C: A.94, N.97, D.98 Chain D: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, P.172, E.175 Ligands: ZN.2 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:N.97, C:D.98, D:N.55, D:G.57, D:S.123, D:T.124, D:S.125, D:S.125, D:S.128 Water bridges: D:N.55, D:N.55, D:S.58 I22.9: 17 residues within 4Å: Chain A: A.94, N.97, D.98 Chain B: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, E.175 Chain C: H.64, E.68, F.73, H.183 Ligands: ZN.10 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.55, B:G.57, B:S.58, B:S.58, B:T.124, B:T.124, B:S.125, B:S.125, B:S.128, A:N.97, A:D.98 Water bridges: B:N.55, B:N.55 I22.11: 18 residues within 4Å: Chain B: H.64, E.68, F.73, H.183 Chain C: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, P.172, E.175 Chain D: A.94, N.97, D.98 Ligands: ZN.8 15 PLIP interactions: 1 interactions with chain B, 12 interactions with chain C, 2 interactions with chain D Water bridges: B:S.71, C:N.55, C:N.55, C:T.124, C:T.124 Hydrogen bonds: C:N.55, C:G.57, C:S.58, C:S.123, C:S.123, C:T.124, C:S.125, C:S.128, D:N.97, D:D.98

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

EDO.7: 3 residues within 4Å: Chain B: T.32, K.35, L.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.32, B:K.35

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

PGE.12: 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

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

PEG.13: 5 residues within 4Å: Chain D: R.28, A.31, T.32, K.35, L.162 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.35

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 1 residues within 4Å: Chain D: D.98 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.98

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

NA.15: 1 residues within 4Å: Ligands: PG4.6 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.47

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