SMTL ID : 5dot.1

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: N.304, Q.324, H.326, E.351, Q.364 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.326, A:E.351, A:E.351, H2O.6 NI.8: 5 residues within 4Å: Chain B: N.304, Q.324, H.326, E.351, Q.364 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.326, B:E.351, B:E.351, H2O.20

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: K.894, W.929, G.953, Q.954 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.929, A:Q.954 Water bridges: A:K.894 EDO.3: 6 residues within 4Å: Chain A: R.803, S.902, E.1023, S.1025, E.1027, R.1028 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.803, A:S.1025 EDO.4: 8 residues within 4Å: Chain A: L.123, D.124, Y.151, G.152, T.793, R.895, E.898, N.952 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.123, A:R.895, A:R.895, A:E.898 EDO.6: 6 residues within 4Å: Chain A: P.76, S.112, N.113, K.116, V.193, I.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113, A:N.113, A:I.216 EDO.9: 7 residues within 4Å: Chain B: K.800, R.803, S.902, E.1023, S.1025, E.1027, R.1028 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.803, B:S.1025 Water bridges: B:S.902, B:S.902

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: S.852, L.853, D.854, K.864, Y.868 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.853, A:D.854, A:K.864, A:Y.868 GOL.7: 4 residues within 4Å: Chain A: P.1288, I.1289, I.1290 Chain B: E.1210 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.1210, A:I.1290, A:I.1290 GOL.10: 5 residues within 4Å: Chain B: S.852, L.853, D.854, K.864, Y.868 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.853, B:D.854, B:Y.868 GOL.11: 5 residues within 4Å: Chain B: K.881, L.883, N.884, C.909, L.910 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.883

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
A

B
B

Carbamoyl-phosphate synthase [ammonia], mitochondrial

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