- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.18 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 11 residues within 4Å:- Chain A: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243
- Chain E: E.53
- Ligands: ADP.1, MG.3
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:S.127, A:S.127, A:W.128, A:E.241, A:N.243
- Salt bridges: A:R.173, A:R.187
PO4.9: 10 residues within 4Å:- Chain C: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243
- Ligands: ADP.8, UN1.10
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:S.127, C:S.127, C:W.128, C:R.187, C:N.243
- Water bridges: C:R.173
- Salt bridges: C:R.173
PO4.12: 12 residues within 4Å:- Chain D: S.127, W.128, R.173, R.187, N.195, D.229, E.241, N.243
- Chain H: E.53
- Ligands: ADP.11, MG.13, MG.14
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:W.128, D:R.187, D:N.195, D:N.243
- Water bridges: D:R.187
- Salt bridges: D:R.173
- 5 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 6 residues within 4Å:- Chain A: R.187, N.195, D.229, E.241
- Ligands: ADP.1, PO4.2
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:D.229, A:E.241
MG.6: 5 residues within 4Å:- Chain B: R.187, D.229, E.241
- Ligands: ADP.4, SO4.5
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:D.229, B:E.241
MG.7: 7 residues within 4Å:- Chain B: K.83, G.126, S.127, E.241, N.243
- Ligands: ADP.4, SO4.5
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.241, B:E.241, H2O.3
MG.13: 5 residues within 4Å:- Chain D: D.229, E.241
- Ligands: ADP.11, PO4.12, MG.14
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.229, D:E.241, H2O.8
MG.14: 6 residues within 4Å:- Chain D: K.83, E.241, N.243
- Ligands: ADP.11, PO4.12, MG.13
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:E.241, D:E.241, H2O.8
- 1 x SO4: SULFATE ION(Non-functional Binders)
- 1 x UN1: 2-AMINOHEXANEDIOIC ACID(Non-covalent)
UN1.10: 13 residues within 4Å:- Chain C: W.128, R.173, Y.175, R.187, N.195, T.196, A.197, E.247, F.248, K.249, N.250, A.251
- Ligands: PO4.9
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:T.196, C:E.247
- Hydrogen bonds: C:W.128, C:T.196, C:T.196, C:T.196, C:A.197, C:E.247, C:N.250, C:N.250, C:A.251
- Salt bridges: C:R.187
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yoshida, A. et al., Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. J. Biol. Chem. (2016)
- Release Date
- 2016-09-07
- Peptides
- RimK-related lysine biosynthesis protein: ABCD
Probable lysine biosynthesis protein: EFGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
JE
KF
LG
MH
N
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.18 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 5 x MG: MAGNESIUM ION(Non-covalent)
- 1 x SO4: SULFATE ION(Non-functional Binders)
- 1 x UN1: 2-AMINOHEXANEDIOIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yoshida, A. et al., Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. J. Biol. Chem. (2016)
- Release Date
- 2016-09-07
- Peptides
- RimK-related lysine biosynthesis protein: ABCD
Probable lysine biosynthesis protein: EFGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GB
HC
ID
JE
KF
LG
MH
N