- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NI: NICKEL (II) ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 7 residues within 4Å:- Chain A: E.703, N.705, R.707
- Ligands: MG.3, K.5, PO4.7, ADP.8
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.703, A:E.703, H2O.1
MG.3: 8 residues within 4Å:- Chain A: H.648, Q.689, E.703, N.705
- Ligands: MG.2, K.6, PO4.7, ADP.8
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.703, H2O.5
MG.11: 3 residues within 4Å:- Chain A: Q.1232, E.1244
- Ligands: ADP.9
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.1244, H2O.9
MG.18: 8 residues within 4Å:- Chain B: A.580, L.581, E.703, N.705, R.707
- Ligands: K.21, PO4.23, ADP.24
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.703, B:E.703
MG.19: 7 residues within 4Å:- Chain B: H.648, T.649, Q.689, E.703
- Ligands: K.22, PO4.23, ADP.24
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.703
MG.27: 3 residues within 4Å:- Chain B: Q.1232, E.1244
- Ligands: ADP.25
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.1244, H2O.14
- 9 x K: POTASSIUM ION(Non-covalent)
K.4: 6 residues within 4Å:- Chain A: E.620, N.641, D.643, A.644, V.647, S.652
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:E.620, A:D.643, A:A.644, A:V.647, A:S.652
K.5: 6 residues within 4Å:- Chain A: T.533, E.534, E.703, V.704, N.705
- Ligands: MG.2
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:T.533, A:E.534, A:E.703, A:V.704
K.6: 8 residues within 4Å:- Chain A: E.622, T.649, N.687, Q.689, N.705, S.711
- Ligands: MG.3, PO4.7
No protein-ligand interaction detected (PLIP)K.13: 3 residues within 4Å:- Chain A: L.767, F.770, T.773
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:L.767, A:F.770, A:T.773
K.14: 3 residues within 4Å:- Chain A: K.881, L.883, C.909
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:K.881, A:L.883, A:C.909, H2O.7
K.20: 6 residues within 4Å:- Chain B: E.620, N.641, D.643, A.644, V.647, S.652
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:E.620, B:D.643, B:A.644, B:V.647, B:S.652
K.21: 7 residues within 4Å:- Chain B: T.533, E.534, R.536, E.703, V.704, N.705
- Ligands: MG.18
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:E.703, B:V.704
K.22: 7 residues within 4Å:- Chain B: E.622, T.649, N.687, Q.689, S.711
- Ligands: MG.19, PO4.23
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:T.649, H2O.12
K.29: 6 residues within 4Å:- Chain B: E.1164, H.1184, E.1186, D.1187, A.1188, V.1190
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:H.1184, B:V.1190
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 13 residues within 4Å:- Chain A: L.581, G.582, H.648, T.649, Q.689, E.703, N.705, R.707, R.710
- Ligands: MG.2, MG.3, K.6, ADP.8
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:G.582, A:N.705
- Water bridges: A:R.707, A:R.707, A:R.707, A:R.710
- Salt bridges: A:H.648, A:R.707, A:R.710
PO4.23: 12 residues within 4Å:- Chain B: L.581, G.582, H.648, Q.689, E.703, N.705, R.707, R.710
- Ligands: MG.18, MG.19, K.22, ADP.24
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:G.582, B:T.649, B:N.705
- Water bridges: B:R.710, B:R.710
- Salt bridges: B:H.648, B:R.707, B:R.710
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.8: 25 residues within 4Å:- Chain A: R.536, M.574, R.576, A.580, L.581, G.582, G.583, E.612, K.613, S.614, V.615, T.616, E.620, M.645, G.646, V.647, H.648, T.649, Q.689, I.702, E.703, S.779
- Ligands: MG.2, MG.3, PO4.7
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:L.581, A:G.582, A:G.583, A:K.613, A:V.615, A:T.616, A:E.620, A:G.646, A:T.649, A:Q.689, A:Q.689
- Water bridges: A:R.536, A:H.648, A:H.648
- Salt bridges: A:R.536, A:R.536, A:R.576, A:H.648
ADP.9: 19 residues within 4Å:- Chain A: A.1093, L.1116, R.1118, M.1128, K.1157, F.1158, V.1159, E.1164, A.1188, G.1189, V.1190, H.1191, S.1192, Q.1232, L.1234, I.1243, E.1244, C.1316
- Ligands: MG.11
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:K.1157, A:V.1159, A:E.1164, A:G.1189, A:S.1192, A:S.1192, A:Q.1232, A:Q.1232
- Salt bridges: A:R.1118, A:H.1191
ADP.24: 25 residues within 4Å:- Chain B: R.536, M.574, R.576, A.580, L.581, G.582, G.583, E.612, K.613, S.614, V.615, T.616, E.620, M.645, G.646, V.647, H.648, T.649, Q.689, I.702, E.703, S.779
- Ligands: MG.18, MG.19, PO4.23
15 PLIP interactions:15 interactions with chain B- Hydrogen bonds: B:L.581, B:G.582, B:G.583, B:E.612, B:E.612, B:V.615, B:T.616, B:E.620, B:G.646, B:T.649, B:Q.689
- Salt bridges: B:R.536, B:R.536, B:R.576, B:H.648
ADP.25: 17 residues within 4Å:- Chain B: A.1093, L.1116, M.1128, K.1157, F.1158, V.1159, E.1164, A.1188, G.1189, V.1190, H.1191, S.1192, Q.1232, L.1234, I.1243, E.1244
- Ligands: MG.27
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:K.1157, B:V.1159, B:E.1164, B:G.1189, B:S.1192, B:S.1192, B:Q.1232
- Water bridges: B:N.1246
- Salt bridges: B:H.1191
- 2 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)
NLG.10: 13 residues within 4Å:- Chain A: I.1355, Q.1356, T.1380, E.1381, A.1382, T.1383, W.1399, L.1427, P.1428, T.1432, K.1433, F.1434, N.1438
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:W.1399
- Hydrogen bonds: A:A.1382, A:T.1383, A:T.1383, A:K.1433, A:F.1434, A:N.1438, A:N.1438
NLG.26: 15 residues within 4Å:- Chain B: G.1354, I.1355, Q.1356, T.1380, E.1381, A.1382, T.1383, W.1399, N.1426, L.1427, P.1428, T.1432, K.1433, F.1434, N.1438
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:W.1399
- Hydrogen bonds: B:A.1382, B:T.1383, B:T.1383, B:K.1433, B:F.1434, B:N.1438, B:N.1438
- Water bridges: B:Q.1356, B:R.1360
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- de Cima, S. et al., Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. Sci Rep (2015)
- Release Date
- 2015-12-09
- Peptides
- Carbamoyl-phosphate synthase [ammonia], mitochondrial: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NI: NICKEL (II) ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 9 x K: POTASSIUM ION(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- de Cima, S. et al., Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. Sci Rep (2015)
- Release Date
- 2015-12-09
- Peptides
- Carbamoyl-phosphate synthase [ammonia], mitochondrial: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B