- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x OGA: N-OXALYLGLYCINE(Non-covalent)
OGA.2: 11 residues within 4Å:- Chain A: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238
- Ligands: MN.1
9 PLIP interactions:8 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:F.156
- Water bridges: A:F.156, A:K.174, A:A.226
- Salt bridges: A:K.174, A:H.224, A:H.236, A:H.236, C:H.12
OGA.6: 12 residues within 4Å:- Chain B: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238
- Chain D: H.12
- Ligands: MN.5
12 PLIP interactions:11 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:F.156, B:T.238
- Water bridges: B:Y.147, B:Y.147, B:F.156, B:K.174, B:A.226
- Salt bridges: B:K.174, B:H.224, B:H.236, B:H.236, D:H.12
OGA.11: 11 residues within 4Å:- Chain E: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238
- Ligands: MN.10
11 PLIP interactions:10 interactions with chain E, 1 interactions with chain G- Hydrogen bonds: E:F.156, E:T.238
- Water bridges: E:Y.147, E:F.156, E:K.174, E:A.226
- Salt bridges: E:K.174, E:H.224, E:H.236, E:H.236, G:H.12
OGA.15: 12 residues within 4Å:- Chain F: Y.147, F.156, H.159, D.161, K.174, W.176, H.224, A.226, H.236, T.238
- Chain H: H.12
- Ligands: MN.14
9 PLIP interactions:8 interactions with chain F, 1 interactions with chain H- Hydrogen bonds: F:F.156
- Water bridges: F:F.156, F:K.174, F:A.226
- Salt bridges: F:K.174, F:H.224, F:H.236, F:H.236, H:H.12
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 4 residues within 4Å:- Chain A: W.42, E.43, R.44
- Chain B: R.271
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:E.43, B:R.271
- Water bridges: B:G.272
EDO.4: 5 residues within 4Å:- Chain A: M.278, D.279, H.285
- Chain B: R.18, R.376
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:R.18
- Water bridges: B:D.372, B:L.418, A:D.279, A:D.279
EDO.7: 6 residues within 4Å:- Chain A: G.139, S.140, N.245, R.320, F.324
- Chain B: F.277
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.320
- Water bridges: A:S.140, A:S.140, A:M.141, A:N.245, A:N.245, A:N.245
EDO.8: 8 residues within 4Å:- Chain A: L.273, F.277, M.278
- Chain B: G.139, S.140, N.245, R.320, F.324
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.140, B:N.245, B:R.320
- Water bridges: B:M.141
EDO.9: 4 residues within 4Å:- Chain A: R.271
- Chain B: W.42, E.43, R.44
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.271, B:R.44
- Water bridges: B:Y.38
EDO.12: 4 residues within 4Å:- Chain E: W.42, E.43, R.44
- Chain F: R.271
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:R.271
- Water bridges: F:G.272
EDO.13: 5 residues within 4Å:- Chain E: M.278, D.279, H.285
- Chain F: R.18, R.376
6 PLIP interactions:3 interactions with chain F, 3 interactions with chain E- Hydrogen bonds: F:R.18, E:D.279
- Water bridges: F:D.372, F:L.418, E:D.279, E:D.279
EDO.16: 6 residues within 4Å:- Chain E: G.139, S.140, N.245, R.320, F.324
- Chain F: F.277
7 PLIP interactions:7 interactions with chain E- Hydrogen bonds: E:R.320
- Water bridges: E:S.140, E:S.140, E:M.141, E:N.245, E:N.245, E:N.245
EDO.17: 8 residues within 4Å:- Chain E: L.273, F.277, M.278
- Chain F: G.139, S.140, N.245, R.320, F.324
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:S.140, F:N.245, F:R.320
- Water bridges: F:M.141
EDO.18: 4 residues within 4Å:- Chain E: R.271
- Chain F: W.42, E.43, R.44
4 PLIP interactions:3 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:E.43, F:R.44, E:R.271
- Water bridges: F:Y.38
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)
- Release Date
- 2014-05-14
- Peptides
- BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66: ABEF
60S RIBOSOMAL PROTEIN L8: CDGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
BC
CD
DG
CH
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x OGA: N-OXALYLGLYCINE(Non-covalent)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)
- Release Date
- 2014-05-14
- Peptides
- BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66: ABEF
60S RIBOSOMAL PROTEIN L8: CDGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
BC
CD
DG
CH
D