SMTL ID : 4q0u.1

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 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: ROR.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.117, A:H.119, A:E.124, A:H.199 CO.8: 5 residues within 4Å: Chain B: H.117, H.119, E.124, H.199 Ligands: ROR.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.117, B:H.119, B:E.124, B:H.199 CO.15: 5 residues within 4Å: Chain C: H.117, H.119, E.124, H.199 Ligands: ROR.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.117, C:H.119, C:E.124, C:H.199 CO.22: 5 residues within 4Å: Chain D: H.117, H.119, E.124, H.199 Ligands: ROR.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.117, D:H.119, D:E.124, D:H.199

4 x ROR: L-ribose(Non-covalent)

ROR.2: 15 residues within 4Å: Chain A: F.53, I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, F.245, R.254 Ligands: CO.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.104, A:K.122, A:Q.215, A:E.222, A:R.254 ROR.9: 15 residues within 4Å: Chain B: F.53, I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, F.245, R.254 Ligands: CO.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.104, B:K.122, B:Q.215, B:E.222, B:R.254 ROR.16: 15 residues within 4Å: Chain C: F.53, I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, F.245, R.254 Ligands: CO.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.104, C:K.122, C:K.122, C:Q.215, C:E.222, C:R.254 ROR.23: 15 residues within 4Å: Chain D: F.53, I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, F.245, R.254 Ligands: CO.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.104, D:K.122, D:Q.215, D:E.222, D:R.254

12 x Z6J: alpha-L-ribofuranose(Non-covalent)

Z6J.3: 6 residues within 4Å: Chain A: R.19, D.23, R.27, V.45, N.46, D.47 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.19, A:D.47 Water bridges: A:R.19, A:R.27, A:D.47 Z6J.4: 6 residues within 4Å: Chain A: R.20, D.23, R.27 Chain D: N.63, W.66, S.67 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.63, A:R.27 Water bridges: D:W.66 Z6J.6: 7 residues within 4Å: Chain A: S.138, T.140, P.141, S.142, A.143, K.177, L.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.138, A:S.138, A:A.143 Z6J.10: 6 residues within 4Å: Chain B: R.19, D.23, R.27, V.45, N.46, D.47 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.19, B:D.47 Water bridges: B:R.19, B:R.27, B:D.47 Z6J.11: 6 residues within 4Å: Chain B: R.20, D.23, R.27 Chain C: N.63, W.66, S.67 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.63, B:D.23, B:R.27 Water bridges: C:W.66 Z6J.13: 7 residues within 4Å: Chain B: S.138, T.140, P.141, S.142, A.143, K.177, L.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.138, B:S.138, B:A.143 Z6J.17: 6 residues within 4Å: Chain C: R.19, D.23, R.27, V.45, N.46, D.47 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.19, C:D.47 Water bridges: C:R.19, C:R.27, C:D.47 Z6J.18: 6 residues within 4Å: Chain B: N.63, W.66, S.67 Chain C: R.20, D.23, R.27 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.23, C:R.27, B:N.63 Water bridges: B:W.66 Z6J.20: 7 residues within 4Å: Chain C: S.138, T.140, P.141, S.142, A.143, K.177, L.198 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.138, C:S.138, C:A.143 Z6J.24: 6 residues within 4Å: Chain D: R.19, D.23, R.27, V.45, N.46, D.47 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.19, D:D.47 Water bridges: D:R.19, D:R.27, D:D.47 Z6J.25: 6 residues within 4Å: Chain A: N.63, W.66, S.67 Chain D: R.20, D.23, R.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.63, D:R.27 Water bridges: A:W.66 Z6J.27: 7 residues within 4Å: Chain D: S.138, T.140, P.141, S.142, A.143, K.177, L.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.138, D:S.138, D:A.143

4 x 0MK: beta-L-ribopyranose(Non-covalent)

0MK.5: 3 residues within 4Å: Chain A: W.161, Y.175, E.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:E.176 Water bridges: A:E.176 0MK.12: 3 residues within 4Å: Chain B: W.161, Y.175, E.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.176 Water bridges: B:E.176 0MK.19: 3 residues within 4Å: Chain C: W.161, Y.175, E.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.176 Water bridges: C:E.176 0MK.26: 3 residues within 4Å: Chain D: W.161, Y.175, E.176 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.176, D:E.176 Water bridges: D:E.176

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

NCO.7: 5 residues within 4Å: Chain A: D.244, F.245, V.246, D.248, N.251 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.244, A:D.244, A:V.246, A:D.248, A:D.248, A:N.251 NCO.14: 5 residues within 4Å: Chain B: D.244, F.245, V.246, D.248, N.251 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.244, B:D.244, B:V.246, B:D.248, B:D.248, B:N.251 NCO.21: 5 residues within 4Å: Chain C: D.244, F.245, V.246, D.248, N.251 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.244, C:D.244, C:V.246, C:D.248, C:D.248, C:N.251 NCO.28: 5 residues within 4Å: Chain D: D.244, F.245, V.246, D.248, N.251 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.244, D:D.244, D:V.246, D:D.248, D:D.248, D:N.251

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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