SMTL ID : 5lu6.1

Heptose isomerase mutant - H64Q

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-tetramer

Ligands

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

I22.1: 16 residues within 4Å: Chain A: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, P.172, Q.175 Chain B: N.97, D.98 Chain D: E.68, R.72, F.73, H.183 18 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:N.55, A:G.57, A:S.58, A:S.123, A:S.123, A:T.124, A:S.125, A:S.128, A:Q.175, D:R.72, D:H.183, B:N.97, B:D.98 Water bridges: A:N.55, A:N.55, A:G.56, A:T.124, A:T.124 I22.4: 13 residues within 4Å: Chain A: N.97, D.98 Chain B: N.55, G.56, G.57, S.123, T.124, S.125, S.128, T.171, Q.175 Chain C: R.72, F.73 20 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:N.55, B:G.57, B:S.123, B:S.123, B:T.124, B:T.124, B:S.125, B:S.128, B:T.171, B:T.171, B:Q.175, A:N.97, A:D.98 Water bridges: B:N.55, B:N.55, B:S.58, B:S.125, B:S.125, C:R.72, C:R.72 I22.7: 15 residues within 4Å: Chain B: E.68, 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 16 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:N.97, D:D.98, C:N.55, C:G.57, C:S.123, C:T.124, C:T.124, C:S.125, C:S.128, C:Q.175, B:E.68 Water bridges: C:N.55, C:N.55, C:G.56, C:S.58, C:T.171 I22.9: 16 residues within 4Å: Chain A: E.68, R.72, F.73 Chain C: N.97, D.98 Chain D: N.55, G.56, G.57, S.58, S.123, T.124, S.125, S.128, T.171, P.172, Q.175 15 PLIP interactions: 1 interactions with chain A, 12 interactions with chain D, 2 interactions with chain C Water bridges: A:R.72, D:N.55, D:N.55 Hydrogen bonds: D:N.55, D:G.57, D:S.58, D:S.58, D:S.123, D:T.124, D:T.124, D:S.125, D:S.128, D:Q.175, C:N.97, C:D.98

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

EDO.2: 4 residues within 4Å: Chain A: K.35, D.161, L.162 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:D.161 EDO.8: 3 residues within 4Å: Chain C: A.14, Q.17, R.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.17 EDO.10: 4 residues within 4Å: Chain D: R.157, C.160, D.161, L.163 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.157, D:D.161 Water bridges: D:L.163 EDO.11: 2 residues within 4Å: Chain D: Q.17, R.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.17, D:R.18 EDO.12: 2 residues within 4Å: Chain D: R.157, E.158 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.157

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.28, A.31, T.32, K.35 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.28, A:K.35 GOL.5: 7 residues within 4Å: Chain B: T.32, R.157, C.160, D.161, L.162, L.163 Ligands: PGE.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.157, B:L.163, B:L.163 Water bridges: B:T.32 GOL.13: 4 residues within 4Å: Chain D: G.113, N.114, E.115, K.141 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.114, D:E.115, D:K.141, D:K.141

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

PGE.6: 6 residues within 4Å: Chain B: A.31, T.32, K.35, D.161, L.162 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.35 Water bridges: B:T.32

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