SMTL ID : 4gji.1

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x RNS: L-RHAMNOSE(Non-covalent)

RNS.1: 12 residues within 4Å: Chain A: W.57, W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Chain B: F.66 Ligands: MN.3, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.57 Water bridges: A:E.219, A:N.283, B:R.65 RNS.6: 13 residues within 4Å: Chain A: F.66 Chain B: W.57, W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Ligands: RM4.5, MN.9, MN.10 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.57 Water bridges: B:N.101, B:E.219, B:N.283, A:R.65 RNS.11: 12 residues within 4Å: Chain C: W.57, W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Chain D: F.66 Ligands: MN.13, MN.14 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:R.65, C:E.219, C:N.283 Hydrophobic interactions: C:W.57 Hydrogen bonds: C:E.219 RNS.17: 14 residues within 4Å: Chain C: F.66 Chain D: W.57, W.104, W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Ligands: RM4.16, MN.19, MN.20 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Water bridges: C:R.65, D:E.219 Hydrophobic interactions: D:W.57, D:W.104

4 x RAM: alpha-L-rhamnopyranose(Non-covalent)

RAM.2: 4 residues within 4Å: Chain A: T.193, R.194, E.197 Chain C: R.315 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:E.197 Water bridges: C:D.311 Salt bridges: C:R.315 RAM.7: 7 residues within 4Å: Chain A: R.65, F.66 Chain B: W.57, G.62, G.63, Q.328, S.329 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.63, B:Q.328, A:R.65 Water bridges: B:W.57, B:G.60, B:S.329, B:S.329 Hydrophobic interactions: A:F.66 RAM.12: 6 residues within 4Å: Chain C: W.57, G.62, G.63, Q.328, S.329 Chain D: F.66 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.63, C:Q.328 Water bridges: C:W.57, C:G.60, C:S.329 Hydrophobic interactions: D:F.66 RAM.18: 8 residues within 4Å: Chain D: F.50, L.309, E.313, F.320, H.321, P.322, H.324, Y.350 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.50, D:L.309, D:Y.350 Hydrogen bonds: D:E.313, D:F.320 Water bridges: D:P.322

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

MN.3: 6 residues within 4Å: Chain A: E.219, D.254, H.257, H.281, D.327 Ligands: RNS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.219, A:D.254, A:H.281, A:D.327 MN.4: 5 residues within 4Å: Chain A: K.221, D.254, H.257, D.289 Ligands: RNS.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.257, A:D.289, H2O.1, H2O.3 MN.9: 7 residues within 4Å: Chain B: E.219, D.254, H.257, H.281, D.327 Ligands: RM4.5, RNS.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.219, B:D.254, B:H.281, B:D.327 MN.10: 6 residues within 4Å: Chain B: K.221, D.254, H.257, D.289 Ligands: RM4.5, RNS.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.257, B:D.289, H2O.19, H2O.22 MN.13: 6 residues within 4Å: Chain C: E.219, D.254, H.257, H.281, D.327 Ligands: RNS.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.219, C:D.254, C:H.281, C:D.327 MN.14: 6 residues within 4Å: Chain C: K.221, D.254, H.257, D.289, D.291 Ligands: RNS.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.257, C:D.289, H2O.40, H2O.42 MN.15: 2 residues within 4Å: Chain B: E.298 Chain C: E.298 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:E.298, C:E.298, H2O.46, H2O.52, H2O.52 MN.19: 7 residues within 4Å: Chain D: E.219, D.254, H.257, H.281, D.327 Ligands: RM4.16, RNS.17 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.219, D:D.254, D:H.281, D:D.327 MN.20: 6 residues within 4Å: Chain D: K.221, D.254, H.257, D.289 Ligands: RM4.16, RNS.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.257, D:D.289, H2O.56, H2O.57 MN.21: 2 residues within 4Å: Chain A: E.298 Chain D: E.298 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:E.298, A:E.298, H2O.63, H2O.70, H2O.70

3 x RM4: beta-L-rhamnopyranose(Non-covalent)

RM4.5: 13 residues within 4Å: Chain A: F.66 Chain B: W.57, W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Ligands: RNS.6, MN.9, MN.10 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.219 Water bridges: B:N.127, B:E.219, B:D.254, B:N.283, B:D.291 Salt bridges: B:K.221, B:H.257 Hydrophobic interactions: A:F.66 RM4.8: 5 residues within 4Å: Chain B: R.5, D.83, R.115, R.414, E.418 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.5, B:R.5, B:D.83, B:R.115 Water bridges: B:D.83, B:D.83, B:E.418, B:R.419, B:R.419 Salt bridges: B:R.5, B:R.414 RM4.16: 13 residues within 4Å: Chain C: F.66, I.429 Chain D: W.179, E.219, K.221, D.254, H.257, H.281, D.289, D.327 Ligands: RNS.17, MN.19, MN.20 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:F.66, C:I.429 Water bridges: C:R.65, D:N.127, D:E.219, D:D.254 Hydrogen bonds: D:E.219 Salt bridges: D:K.221, D:H.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, H. et al., Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. FEBS Open Bio (2013)

Release Date

2012-12-12

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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