SMTL ID : 5dou.2 (1 other biounit)

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 7 residues within 4Å: Chain A: N.304, Q.324, H.326, N.344, T.349, N.350, E.351 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.326, A:E.351, A:E.351 NI.13: 5 residues within 4Å: Chain B: N.304, Q.324, H.326, E.351, Q.364 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.326, B:E.351, B:E.351

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: A.580, L.581, E.703, N.705, R.707 Ligands: K.5, PO4.7, ADP.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.703, A:E.703 MG.3: 7 residues within 4Å: Chain A: H.648, T.649, Q.689, E.703 Ligands: K.6, PO4.7, ADP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.703 MG.11: 3 residues within 4Å: Chain A: Q.1232, E.1244 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.1244 MG.14: 7 residues within 4Å: Chain B: A.580, E.703, N.705 Ligands: MG.15, K.17, PO4.19, ADP.20 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.703, B:E.703 MG.15: 7 residues within 4Å: Chain B: H.648, Q.689, E.703 Ligands: MG.14, K.18, PO4.19, ADP.20 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.703 MG.23: 3 residues within 4Å: Chain B: Q.1232, E.1244 Ligands: ADP.21 No protein-ligand interaction detected (PLIP)

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: 7 residues within 4Å: Chain A: T.533, E.534, R.536, E.703, V.704, N.705 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.533, A:E.703 K.6: 9 residues within 4Å: Chain A: E.622, T.649, N.687, Q.689, N.705, R.710, S.711 Ligands: MG.3, PO4.7 No protein-ligand interaction detected (PLIP) K.12: 7 residues within 4Å: Chain A: E.1164, H.1184, E.1186, D.1187, A.1188, V.1190 Ligands: ADP.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.1164, A:H.1184, A:D.1187, A:V.1190 K.16: 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.17: 7 residues within 4Å: Chain B: T.533, E.534, R.536, E.703, V.704, N.705 Ligands: MG.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.533, B:E.703, B:V.704 K.18: 7 residues within 4Å: Chain B: E.622, T.649, N.687, Q.689, S.711 Ligands: MG.15, PO4.19 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.649, H2O.9 K.25: 3 residues within 4Å: Chain B: K.881, L.883, C.909 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.881, B:L.883, B:C.909, H2O.9 K.26: 3 residues within 4Å: Chain B: L.767, F.770, T.773 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.767, B:F.770, B:T.773

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 12 residues within 4Å: Chain A: L.581, G.582, H.648, Q.689, E.703, N.705, R.707, R.710 Ligands: MG.2, MG.3, K.6, ADP.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.582, A:N.705, A:N.705 Water bridges: A:R.710 Salt bridges: A:H.648, A:R.707, A:R.710 PO4.19: 12 residues within 4Å: Chain B: L.581, G.582, H.648, Q.689, E.703, N.705, R.707, R.710 Ligands: MG.14, MG.15, K.18, ADP.20 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.582, B:T.649, B:Q.689, B:N.705 Water bridges: 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:L.581, A:G.582, A:G.583, A:E.612, A:V.615, A:T.616, A:E.620, A:G.646, A:T.649, A:Q.689 Water bridges: A:R.536, A:A.580 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, 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, K.12 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:E.1244 Salt bridges: A:R.1118, A:H.1191 ADP.20: 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.14, MG.15, PO4.19 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.581, B:G.582, B:G.583, B:E.612, B:K.613, B:V.615, B:T.616, B:E.620, B:G.646, B:T.649, B:Q.689, B:E.703 Salt bridges: B:R.536, B:R.536, B:R.576, B:H.648 ADP.21: 17 residues within 4Å: Chain B: A.1093, L.1116, R.1118, 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.23 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.1157, B:V.1159, B:E.1164, B:G.1189, B:S.1192, B:Q.1232, B:Q.1232, B:E.1244 Water bridges: B:N.1246 Salt bridges: B:R.1118, B:H.1191

2 x NLG: N-ACETYL-L-GLUTAMATE(Non-covalent)

NLG.10: 13 residues within 4Å: Chain A: G.1354, I.1355, Q.1356, T.1380, E.1381, A.1382, T.1383, W.1399, L.1427, T.1432, K.1433, F.1434, N.1438 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.1399 Hydrogen bonds: A:T.1380, A:A.1382, A:T.1383, A:T.1383, A:T.1383, A:K.1433, A:F.1434, A:N.1438, A:N.1438 Water bridges: A:R.1360 NLG.22: 14 residues within 4Å: Chain B: 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:T.1380, B:A.1382, B:T.1383, B:T.1383, B:T.1383, B:K.1433, B:F.1434, B:N.1438, B:N.1438

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.24: 3 residues within 4Å: Chain B: R.1248, S.1250, R.1251 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.27: 10 residues within 4Å: Chain B: A.319, F.320, I.321, D.375, D.631, N.632, C.633, R.671, I.674, R.678 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.321, B:I.321, B:D.375, B:D.631, B:C.633, B:R.671, B:R.671, B:R.678, B:R.678

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
C

B
D

Carbamoyl-phosphate synthase [ammonia], mitochondrial

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