SMTL ID : 4q0s.1

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with ribitol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.117, H.119, E.124, H.199 Ligands: RB0.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.117, A:H.119, A:E.124, A:H.199 CO.5: 5 residues within 4Å: Chain B: H.117, H.119, E.124, H.199 Ligands: RB0.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.117, B:H.119, B:E.124, B:H.199 CO.9: 5 residues within 4Å: Chain C: H.117, H.119, E.124, H.199 Ligands: RB0.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.117, C:H.119, C:E.124, C:H.199 CO.13: 5 residues within 4Å: Chain D: H.117, H.119, E.124, H.199 Ligands: RB0.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.117, D:H.119, D:E.124, D:H.199

8 x RB0: D-ribitol(Non-covalent)

RB0.2: 16 residues within 4Å: Chain A: F.53, I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, Y.126, H.199, F.201, E.215, E.222, R.254 Ligands: CO.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.122, A:Y.126, A:E.222, A:R.254 RB0.3: 6 residues within 4Å: Chain A: M.155, P.156, P.189, K.190, F.191, V.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.190, A:V.192, A:V.192 RB0.6: 16 residues within 4Å: Chain B: F.53, I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, Y.126, H.199, F.201, E.215, E.222, R.254 Ligands: CO.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.122, B:E.222, B:R.254 RB0.7: 6 residues within 4Å: Chain B: M.155, P.156, P.189, K.190, F.191, V.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.190, B:V.192, B:V.192 RB0.10: 16 residues within 4Å: Chain C: F.53, I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, Y.126, H.199, F.201, E.215, E.222, R.254 Ligands: CO.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.122, C:E.222, C:R.254 RB0.11: 6 residues within 4Å: Chain C: M.155, P.156, P.189, K.190, F.191, V.192 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.190, C:V.192, C:V.192 RB0.14: 16 residues within 4Å: Chain D: F.53, I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, Y.126, H.199, F.201, E.215, E.222, R.254 Ligands: CO.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.122, D:Y.126, D:E.222, D:R.254 RB0.15: 6 residues within 4Å: Chain D: M.155, P.156, P.189, K.190, F.191, V.192 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.190, D:V.192, D:V.192

4 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.4: 4 residues within 4Å: Chain A: D.244, F.245, V.246, D.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.245, A:V.246, A:V.246 NCO.8: 4 residues within 4Å: Chain B: D.244, F.245, V.246, D.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.245, B:V.246, B:V.246 NCO.12: 4 residues within 4Å: Chain C: D.244, F.245, V.246, D.248 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.245, C:V.246, C:V.246 NCO.16: 4 residues within 4Å: Chain D: D.244, F.245, V.246, D.248 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.245, D:V.246, D:V.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, H. et al., X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate. Febs J. (2014)

Release Date

2014-05-28

Peptides

L-Ribose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-Ribose isomerase

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