SMTL ID : 8jq5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 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: PSJ.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: PSJ.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.264, A:D.296, A:D.298, H2O.1, H2O.1 MN.5: 6 residues within 4Å: Chain B: E.228, D.261, H.264, H.288, D.328 Ligands: PSJ.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: PSJ.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.9, H2O.9 MN.8: 7 residues within 4Å: Chain C: E.228, D.261, H.264, H.288, D.328 Ligands: PSJ.10, PSV.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.228, C:D.261, C:H.288, C:D.328 MN.9: 6 residues within 4Å: Chain C: D.261, H.264, D.296, D.298 Ligands: PSJ.10, PSV.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.264, C:D.296, C:D.298, H2O.17, H2O.17 MN.13: 7 residues within 4Å: Chain D: E.228, D.261, H.264, H.288, D.328 Ligands: PSJ.15, PSV.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.228, D:D.261, D:H.288, D:D.328 MN.14: 6 residues within 4Å: Chain D: D.261, H.264, D.296, D.298 Ligands: PSJ.15, PSV.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.264, D:D.296, D:D.298, H2O.24, H2O.25

4 x PSJ: D-psicose(Non-covalent)

PSJ.3: 16 residues within 4Å: Chain A: W.42, I.47, I.61, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.1, MN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.228, A:K.230, A:D.328 Water bridges: A:N.185, A:E.228 PSJ.7: 16 residues within 4Å: Chain B: W.42, I.47, I.61, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.5, MN.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.228, B:K.230, B:D.328 Water bridges: B:H.97, B:E.228 PSJ.10: 16 residues within 4Å: Chain C: W.42, I.47, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.8, MN.9, PSV.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.228 Water bridges: C:N.185, C:D.298, C:D.328 PSJ.15: 16 residues within 4Å: Chain D: W.42, I.47, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.13, MN.14, PSV.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.230, D:D.328 Water bridges: D:N.185, D:E.228, D:K.230

4 x PSV: alpha-D-psicofuranose(Non-covalent)

PSV.4: 3 residues within 4Å: Chain A: K.144, D.153, K.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.144 PSV.11: 15 residues within 4Å: Chain C: W.42, I.47, H.97, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.8, MN.9, PSJ.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.228, C:D.296 Water bridges: C:N.185 PSV.12: 7 residues within 4Å: Chain C: K.91, H.92, R.93, G.128, V.129, G.130, S.180 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.91, C:R.93, C:G.130, C:S.180, C:S.180 PSV.16: 16 residues within 4Å: Chain D: W.42, I.47, H.97, F.138, W.187, E.228, K.230, D.261, H.264, H.288, D.296, D.328, F.330 Ligands: MN.13, MN.14, PSJ.15 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.228, D:E.228, D:K.230 Water bridges: D:N.185, D:E.228, 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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