SMTL ID : 8jq3.1

Crystal structure of L-rhamnose isomerase from Lactobacillus rhamnosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.228, D.261, H.288, D.328 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.228, A:D.261, A:H.288, A:D.328 MN.2: 3 residues within 4Å: Chain A: H.264, D.296, D.298 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.264, A:D.296, A:D.298, H2O.1, H2O.1, H2O.4 MN.3: 4 residues within 4Å: Chain B: E.228, D.261, H.288, D.328 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.228, B:D.261, B:H.288, B:D.328 MN.4: 4 residues within 4Å: Chain B: D.261, H.264, D.296, D.298 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.264, B:D.296, B:D.298, H2O.7, H2O.8, H2O.11 MN.5: 4 residues within 4Å: Chain C: E.228, D.261, H.288, D.328 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.228, C:D.261, C:H.288, C:D.328 MN.6: 3 residues within 4Å: Chain C: H.264, D.296, D.298 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.264, C:D.296, C:D.298, H2O.16, H2O.16, H2O.16 MN.7: 4 residues within 4Å: Chain D: E.228, D.261, H.288, D.328 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.228, D:D.261, D:H.288, D:D.328 MN.8: 3 residues within 4Å: Chain D: H.264, D.296, D.298 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.264, D:D.296, D:D.298, H2O.22, H2O.23, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, H. et al., X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase. Appl.Microbiol.Biotechnol. (2024)

Release Date

2024-03-13

Peptides

L-rhamnose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-rhamnose isomerase

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