- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.93 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CO: COBALT (II) ION(Non-covalent)
- 8 x 0MK: beta-L-ribopyranose(Non-covalent)
0MK.2: 14 residues within 4Å:- Chain A: I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, E.215, S.220, E.222, N.243, R.254
- Ligands: CO.1
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:K.122, A:E.215, A:E.215, A:S.220, A:S.220, A:N.243, A:R.254
- Water bridges: A:K.104, A:S.220
- Salt bridges: A:H.117, A:H.119, A:K.122
0MK.5: 4 residues within 4Å:- Chain A: W.161, Y.175, E.176, T.179
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.176, A:E.176, A:E.176
- Water bridges: A:W.161
0MK.8: 14 residues within 4Å:- Chain B: I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, E.215, S.220, E.222, N.243, R.254
- Ligands: CO.7
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:K.122, B:E.215, B:E.215, B:S.220, B:S.220, B:N.243, B:R.254
- Water bridges: B:K.104, B:S.220
- Salt bridges: B:H.117, B:H.119, B:K.122
0MK.11: 4 residues within 4Å:- Chain B: W.161, Y.175, E.176, T.179
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.176, B:E.176
- Water bridges: B:W.161
0MK.14: 14 residues within 4Å:- Chain C: I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, E.215, S.220, E.222, N.243, R.254
- Ligands: CO.13
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:K.122, C:E.215, C:E.215, C:S.220, C:S.220, C:N.243, C:R.254
- Water bridges: C:K.104, C:S.220
- Salt bridges: C:H.117, C:H.119, C:K.122
0MK.17: 4 residues within 4Å:- Chain C: W.161, Y.175, E.176, T.179
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:E.176, C:E.176
- Water bridges: C:W.161
0MK.20: 14 residues within 4Å:- Chain D: I.76, K.104, M.106, C.114, H.117, H.119, K.122, E.124, E.215, S.220, E.222, N.243, R.254
- Ligands: CO.19
12 PLIP interactions:12 interactions with chain D- Hydrogen bonds: D:K.122, D:E.215, D:E.215, D:S.220, D:S.220, D:N.243, D:R.254
- Water bridges: D:K.104, D:S.220
- Salt bridges: D:H.117, D:H.119, D:K.122
0MK.23: 4 residues within 4Å:- Chain D: W.161, Y.175, E.176, T.179
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:E.176, D:E.176, D:E.176
- Water bridges: D:W.161
- 8 x Z6J: alpha-L-ribofuranose(Non-covalent)
Z6J.3: 6 residues within 4Å:- Chain A: R.19, D.23, E.42, V.45, N.46, D.47
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:R.19, A:E.42, A:D.47
- Water bridges: 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
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:N.63, A:R.27
Z6J.9: 6 residues within 4Å:- Chain B: R.19, D.23, E.42, V.45, N.46, D.47
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.19, B:E.42, B:D.47
- Water bridges: B:R.27, B:D.47
Z6J.10: 6 residues within 4Å:- Chain B: R.20, D.23, R.27
- Chain C: N.63, W.66, S.67
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:D.23, B:R.27, C:N.63
Z6J.15: 6 residues within 4Å:- Chain C: R.19, D.23, E.42, V.45, N.46, D.47
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:R.19, C:E.42, C:D.47
- Water bridges: C:R.27, C:D.47
Z6J.16: 6 residues within 4Å:- Chain B: N.63, W.66, S.67
- Chain C: R.20, D.23, R.27
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:D.23, C:R.27, B:N.63
Z6J.21: 6 residues within 4Å:- Chain D: R.19, D.23, E.42, V.45, N.46, D.47
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:R.19, D:E.42, D:D.47
- Water bridges: D:R.27, D:D.47
Z6J.22: 6 residues within 4Å:- Chain A: N.63, W.66, S.67
- Chain D: R.20, D.23, R.27
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:R.27, A:N.63
- 4 x NCO: COBALT HEXAMMINE(III)(Non-covalent)
NCO.6: 4 residues within 4Å:- Chain A: D.244, F.245, V.246, D.248
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.244, A:D.244, A:V.246, A:V.246, A:D.248
NCO.12: 4 residues within 4Å:- Chain B: D.244, F.245, V.246, D.248
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:D.244, B:D.244, B:V.246, B:V.246, B:D.248
NCO.18: 4 residues within 4Å:- Chain C: D.244, F.245, V.246, D.248
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:D.244, C:D.244, C:V.246, C:V.246, C:D.248
NCO.24: 4 residues within 4Å:- Chain D: D.244, F.245, V.246, D.248
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:D.244, D:D.244, D:V.246, D:V.246, D:D.248
- 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 1.93 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CO: COBALT (II) ION(Non-covalent)
- 8 x 0MK: beta-L-ribopyranose(Non-covalent)
- 8 x Z6J: alpha-L-ribofuranose(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