- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.98 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CO: COBALT (II) ION(Non-covalent)
- 8 x QDK: L-ribulose(Non-covalent)
QDK.2: 13 residues within 4Å:- Chain A: I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, R.254
- Ligands: CO.1
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:K.104, A:K.104, A:K.122, A:Y.126, A:Q.215, A:Q.215, A:R.254
- Water bridges: A:N.243
QDK.4: 7 residues within 4Å:- Chain A: K.43, M.44, E.78, S.79, L.80, N.81, E.82
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.78, A:N.81
QDK.11: 13 residues within 4Å:- Chain B: I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, R.254
- Ligands: CO.10
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:K.104, B:K.104, B:K.122, B:Q.215, B:Q.215, B:R.254
- Water bridges: B:N.243
QDK.13: 7 residues within 4Å:- Chain B: K.43, M.44, E.78, S.79, L.80, N.81, E.82
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.78, B:E.78, B:N.81
- Water bridges: B:T.41
QDK.20: 13 residues within 4Å:- Chain C: I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, R.254
- Ligands: CO.19
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:K.104, C:K.104, C:K.122, C:Q.215, C:Q.215, C:R.254
- Water bridges: C:N.243
QDK.22: 7 residues within 4Å:- Chain C: K.43, M.44, E.78, S.79, L.80, N.81, E.82
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.78, C:E.78, C:N.81
- Water bridges: C:T.41
QDK.29: 13 residues within 4Å:- Chain D: I.76, K.104, C.114, H.117, H.119, K.122, E.124, H.199, F.201, Q.215, E.222, R.254
- Ligands: CO.28
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:K.104, D:K.104, D:K.122, D:Y.126, D:Q.215, D:Q.215, D:R.254
- Water bridges: D:N.243
QDK.31: 7 residues within 4Å:- Chain D: K.43, M.44, E.78, S.79, L.80, N.81, E.82
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.78, D:N.81
- 20 x RUU: alpha-L-ribulofuranose(Non-covalent)
RUU.3: 9 residues within 4Å:- Chain A: M.44, N.46, S.48, A.49, I.76, F.77, E.78, T.224, A.226
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.46, A:I.76, A:I.76, A:E.78
RUU.5: 7 residues within 4Å:- Chain A: R.19, Y.22, D.23, R.27, V.45, N.46, D.47
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.19, A:R.27, A:R.27
- Water bridges: A:D.47
RUU.6: 7 residues within 4Å:- Chain A: R.19, R.20, D.23, R.27
- Chain D: N.63, W.66, S.67
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.19, A:D.23, A:R.27, A:R.27
- Water bridges: A:R.20, A:D.23, A:D.23
RUU.7: 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:P.162
RUU.8: 6 residues within 4Å:- Chain A: S.138, T.140, P.141, S.142, K.177, L.198
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.138
RUU.12: 9 residues within 4Å:- Chain B: M.44, N.46, S.48, A.49, I.76, F.77, E.78, T.224, A.226
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:N.46, B:I.76, B:I.76, B:E.78, B:T.224
RUU.14: 7 residues within 4Å:- Chain B: R.19, Y.22, D.23, R.27, V.45, N.46, D.47
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.19, B:R.27, B:R.27
- Water bridges: B:D.47
RUU.15: 7 residues within 4Å:- Chain B: R.19, R.20, D.23, R.27
- Chain C: N.63, W.66, S.67
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:R.19, B:D.23, B:D.23, B:R.27, B:R.27
- Water bridges: B:T.18, B:D.23, B:D.23
RUU.16: 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:P.162
RUU.17: 6 residues within 4Å:- Chain B: S.138, T.140, P.141, S.142, K.177, L.198
1 PLIP interactions:1 interactions with chain B- Water bridges: B:S.138
RUU.21: 9 residues within 4Å:- Chain C: M.44, N.46, S.48, A.49, I.76, F.77, E.78, T.224, A.226
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:N.46, C:I.76, C:I.76, C:E.78, C:T.224
RUU.23: 7 residues within 4Å:- Chain C: R.19, Y.22, D.23, R.27, V.45, N.46, D.47
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:R.19, C:R.27, C:R.27
- Water bridges: C:D.47
RUU.24: 7 residues within 4Å:- Chain B: N.63, W.66, S.67
- Chain C: R.19, R.20, D.23, R.27
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:R.19, C:D.23, C:D.23, C:R.27, C:R.27
- Water bridges: C:T.18, C:D.23, C:D.23
RUU.25: 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:P.162
RUU.26: 6 residues within 4Å:- Chain C: S.138, T.140, P.141, S.142, K.177, L.198
1 PLIP interactions:1 interactions with chain C- Water bridges: C:S.138
RUU.30: 9 residues within 4Å:- Chain D: M.44, N.46, S.48, A.49, I.76, F.77, E.78, T.224, A.226
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:N.46, D:I.76, D:I.76, D:E.78
RUU.32: 7 residues within 4Å:- Chain D: R.19, Y.22, D.23, R.27, V.45, N.46, D.47
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.19, D:R.27, D:R.27
- Water bridges: D:D.47
RUU.33: 7 residues within 4Å:- Chain A: N.63, W.66, S.67
- Chain D: R.19, R.20, D.23, R.27
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:R.19, D:D.23, D:R.27, D:R.27
- Water bridges: D:R.20, D:D.23, D:D.23
RUU.34: 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:P.162
RUU.35: 6 residues within 4Å:- Chain D: S.138, T.140, P.141, S.142, K.177, L.198
1 PLIP interactions:1 interactions with chain D- Water bridges: D:S.138
- 4 x NCO: COBALT HEXAMMINE(III)(Non-covalent)
NCO.9: 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:F.245, A:V.246, A:V.246, A:D.248, A:N.251
NCO.18: 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:F.245, B:V.246, B:V.246, B:D.248, B:N.251
NCO.27: 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:F.245, C:V.246, C:V.246, C:D.248, C:N.251
NCO.36: 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:F.245, D:V.246, D:V.246, 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
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.98 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CO: COBALT (II) ION(Non-covalent)
- 8 x QDK: L-ribulose(Non-covalent)
- 20 x RUU: alpha-L-ribulofuranose(Non-covalent)
- 4 x NCO: COBALT HEXAMMINE(III)(Non-covalent)
- 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
AB
AC
AD
A