SMTL ID : 7e4s.1

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with HEPES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-hexamer

Ligands

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 15 residues within 4Å: Chain A: R.163, I.165, T.184, N.193, T.194, H.198, H.200, R.203, E.205, Y.207, F.258, W.260, M.262, Y.269 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.194, A:T.194, A:R.203 Salt bridges: A:R.163, A:E.205, A:E.205 pi-Cation interactions: A:W.260 EPE.3: 12 residues within 4Å: Chain B: R.163, I.165, T.184, T.194, H.198, H.200, R.203, E.205, W.260, M.262, M.272 Ligands: ZN.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.184, B:T.184, B:T.194, B:R.203, B:R.203 Salt bridges: B:R.163, B:E.205, B:E.205 pi-Cation interactions: B:W.260 EPE.5: 15 residues within 4Å: Chain C: R.163, I.165, T.184, N.193, T.194, M.195, H.198, R.203, E.205, F.258, W.260, M.262, Y.269, M.272 Ligands: ZN.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.194, C:T.194, C:R.203, C:Y.207, C:Y.269 Salt bridges: C:R.163, C:E.205, C:E.205 EPE.7: 11 residues within 4Å: Chain D: R.163, I.165, T.184, N.193, T.194, E.205, Y.207, F.258, W.260, M.262 Ligands: ZN.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.184, D:T.194, D:T.194 Salt bridges: D:R.163, D:E.205, D:E.205 EPE.9: 10 residues within 4Å: Chain E: R.163, I.165, T.184, N.193, T.194, H.200, R.203, E.205, M.262 Ligands: ZN.10 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:T.184, E:T.184, E:T.194, E:R.203 Salt bridges: E:R.163, E:E.205, E:E.205 EPE.11: 13 residues within 4Å: Chain F: R.163, I.165, T.184, N.193, T.194, H.198, H.200, R.203, E.205, W.260, M.262, M.272 Ligands: ZN.12 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.194, F:R.203, F:R.203 Salt bridges: F:R.163, F:E.205, F:E.205

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.198, H.200, E.205, H.248 Ligands: EPE.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.198, A:H.200, A:E.205, A:H.248 ZN.4: 5 residues within 4Å: Chain B: H.198, H.200, E.205, H.248 Ligands: EPE.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.200, B:E.205 ZN.6: 5 residues within 4Å: Chain C: H.198, H.200, E.205, H.248 Ligands: EPE.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.200, C:E.205, C:H.248 ZN.8: 4 residues within 4Å: Chain D: H.200, E.205, H.248 Ligands: EPE.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.205 ZN.10: 4 residues within 4Å: Chain E: H.200, E.205, H.248 Ligands: EPE.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.200, E:E.205 ZN.12: 5 residues within 4Å: Chain F: H.198, H.200, E.205, H.248 Ligands: EPE.11 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.200, F:E.205, F:H.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iwase, H. et al., Crystal structures of Lacticaseibacillus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI in complex with substrate analogs. J.Appl.Glyosci. (2023)

Release Date

2022-02-23

Peptides

5-dehydro-4-deoxy-D-glucuronate isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

5-dehydro-4-deoxy-D-glucuronate isomerase

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