- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.2: 28 residues within 4Å:- Chain A: T.78, T.84, V.85, R.112, T.113, I.135, G.136, G.138, A.139, Q.140, Y.160, D.161, T.162, D.163, A.166, V.201, T.202, A.203, I.210, V.225, G.226, D.228, K.232, S.293, V.294, G.295
- Chain B: K.331
- Ligands: ORN.3
29 PLIP interactions:27 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:T.113, A:Q.140, A:V.225
- Hydrogen bonds: A:R.112, A:A.139, A:Q.140, A:Q.140, A:T.162, A:T.162, A:T.202, A:A.203, A:V.225, A:K.232, B:K.331, B:K.331
- Water bridges: A:T.78, A:T.84, A:T.84, A:T.84, A:T.84, A:V.85, A:G.138, A:S.141, A:D.204, A:D.204, A:D.204, A:D.204, A:K.232, A:S.293
NAD.10: 27 residues within 4Å:- Chain A: K.331
- Chain B: T.78, T.84, V.85, R.112, T.113, G.136, G.138, A.139, Q.140, Y.160, D.161, T.162, D.163, A.166, V.201, T.202, A.203, I.210, V.225, G.226, D.228, K.232, S.293, V.294, G.295
- Ligands: ORN.4
27 PLIP interactions:25 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:T.113, B:Q.140, B:V.225
- Hydrogen bonds: B:R.112, B:A.139, B:Q.140, B:Q.140, B:T.162, B:T.162, B:T.202, B:A.203, B:V.225, B:K.232, A:K.331, A:K.331
- Water bridges: B:T.78, B:T.84, B:T.84, B:T.84, B:T.84, B:T.84, B:G.138, B:S.141, B:D.204, B:D.204, B:K.232, B:S.293
- 2 x ORN: L-ornithine(Non-covalent)
ORN.3: 14 residues within 4Å:- Chain A: R.45, V.54, E.56, M.58, K.69, V.71, N.72, G.73, T.109, R.112, D.228, V.294, G.295
- Ligands: NAD.2
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:V.71
- Hydrogen bonds: A:R.45, A:R.45, A:G.73, A:D.228
- Salt bridges: A:R.45, A:K.69, A:R.112
ORN.4: 14 residues within 4Å:- Chain B: R.45, E.56, M.58, K.69, V.71, N.72, G.73, V.85, T.109, R.112, D.228, V.294, G.295
- Ligands: NAD.10
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:V.71
- Hydrogen bonds: B:R.45, B:R.45, B:N.72, B:D.228
- Salt bridges: B:R.45, B:K.69, B:R.112
- 6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.5: 8 residues within 4Å:- Chain A: Q.38, A.39, F.40, D.41, A.61, D.62, K.63
- Ligands: MPD.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.63
MPD.6: 3 residues within 4Å:- Chain A: Q.38, A.39
- Ligands: MPD.5
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:A.39
MPD.7: 6 residues within 4Å:- Chain A: S.64, R.65, L.91, D.93, V.100, L.308
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:R.65, A:L.91, A:V.100, A:L.308
- Hydrogen bonds: A:D.93
MPD.8: 6 residues within 4Å:- Chain A: Y.3, L.308, A.311, E.312, G.315, M.316
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.3, A:Y.3, A:L.308
MPD.12: 6 residues within 4Å:- Chain B: Y.3, L.308, A.311, E.312, G.315, M.316
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.3, B:L.308, B:E.312
MPD.13: 7 residues within 4Å:- Chain B: S.64, R.65, L.91, A.92, D.93, V.100, L.308
1 PLIP interactions:1 interactions with chain B- Water bridges: B:V.94
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Goodman, J.L. et al., Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications forthe u-Crystallin Family. Biochemistry (2004)
- Release Date
- 2004-11-09
- Peptides
- ornithine cyclodeaminase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 2 x ORN: L-ornithine(Non-covalent)
- 6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Goodman, J.L. et al., Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications forthe u-Crystallin Family. Biochemistry (2004)
- Release Date
- 2004-11-09
- Peptides
- ornithine cyclodeaminase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B