SMTL ID : 8jq6.1

Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: E.228, D.261, H.264, H.288, D.328 Ligands: ALL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.228, A:D.261, A:H.288, A:D.328 MN.2: 5 residues within 4Å: Chain A: D.261, H.264, D.296, D.298 Ligands: ALL.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.264, A:D.298, H2O.1, H2O.1, H2O.1 MN.5: 6 residues within 4Å: Chain B: E.228, D.261, H.264, H.288, D.328 Ligands: ALL.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.228, B:D.261, B:H.288, B:D.328 MN.6: 5 residues within 4Å: Chain B: D.261, H.264, D.296, D.298 Ligands: ALL.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.264, B:D.296, B:D.298, H2O.10, H2O.12 MN.8: 6 residues within 4Å: Chain C: E.228, D.261, H.264, H.288, D.328 Ligands: AFD.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.228, C:D.261, C:H.288, C:D.328 MN.9: 5 residues within 4Å: Chain C: D.261, H.264, D.296, D.298 Ligands: AFD.10 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.264, C:D.296, C:D.298, H2O.20, H2O.20, H2O.20 MN.11: 5 residues within 4Å: Chain D: E.228, D.261, H.288, D.328 Ligands: AFD.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.228, D:D.261, D:H.288, D:D.328 MN.12: 4 residues within 4Å: Chain D: H.264, D.296, D.298 Ligands: AFD.13 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.264, D:D.296, D:D.298, H2O.29, H2O.30, H2O.32

6 x ALL: beta-D-allopyranose(Non-covalent)

ALL.3: 11 residues within 4Å: Chain A: W.42, H.97, W.187, E.228, K.230, D.261, H.264, D.296, D.328 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.97, A:E.228, A:K.230 Water bridges: A:N.185, A:K.230, A:D.298 Salt bridges: A:K.230 ALL.4: 6 residues within 4Å: Chain A: F.403, D.404, M.406, N.407, H.410 Chain B: E.377 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.404, A:D.404, A:N.407, A:N.407, B:E.377 Water bridges: A:V.2, A:D.404, A:H.410 ALL.7: 13 residues within 4Å: Chain B: W.42, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328 Ligands: MN.5, MN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.97, B:E.228, B:K.230, B:H.264 Water bridges: B:N.185, B:K.230, B:D.298 Salt bridges: B:K.230 ALL.14: 6 residues within 4Å: Chain C: N.368, A.369 Chain D: Y.67, P.68, F.418 Ligands: ALL.15 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:N.368, D:Y.67 Water bridges: A:D.145 ALL.15: 4 residues within 4Å: Chain A: D.145 Chain D: N.66, Y.67 Ligands: ALL.14 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.66 Water bridges: A:D.145 ALL.16: 6 residues within 4Å: Chain C: E.377 Chain D: F.403, D.404, M.406, N.407, H.410 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.404, D:N.407, D:H.410, C:E.377

2 x AFD: alpha-D-allopyranose(Non-covalent)

AFD.10: 13 residues within 4Å: Chain C: W.42, H.97, F.138, W.187, E.228, K.230, D.261, H.264, D.296, D.298, D.328 Ligands: MN.8, MN.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.97, C:E.228, C:K.230, C:H.264, C:D.298 Water bridges: C:N.185, C:K.230, C:K.230 Salt bridges: C:K.230 AFD.13: 13 residues within 4Å: Chain D: W.42, H.97, F.138, W.187, E.228, K.230, D.261, H.264, D.296, D.298, D.328 Ligands: MN.11, MN.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.97, D:E.228, D:K.230, D:H.264, D:D.298 Water bridges: D:N.185 Salt bridges: D:K.230

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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