SMTL ID : 1a9x.3 (4 other biounits)

CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: M.174, E.299, N.301 Ligands: MN.2, K.4, PO4.5, ADP.21 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.25 MN.2: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, PO4.5, K.16, ADP.21 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.26 MN.6: 3 residues within 4Å: Chain A: Q.829, E.841 Ligands: ADP.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.841

8 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: E.215, N.236, D.238, A.239, I.242, S.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.215, A:D.238, A:A.239, A:I.242, A:S.247 K.4: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:E.299, A:M.300, H2O.4, H2O.25 K.7: 3 residues within 4Å: Chain A: E.841, N.843 Ligands: ADP.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.841 K.8: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.761, A:H.781, A:Q.784, A:V.787, A:S.792 K.15: 3 residues within 4Å: Chain A: D.84, G.112, T.114 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.84, A:G.112, A:T.114, H2O.25 K.16: 7 residues within 4Å: Chain A: E.217, T.244, N.283, Q.285, S.307 Ligands: MN.2, PO4.5 No protein-ligand interaction detected (PLIP) K.17: 3 residues within 4Å: Chain A: T.143, A.144, R.145 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.143, A:T.143, H2O.20, H2O.20 K.26: 2 residues within 4Å: Chain B: H.15, D.111 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.15, B:D.111, H2O.30

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

PO4.5: 12 residues within 4Å: Chain A: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.1, MN.2, K.16, ADP.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.175, A:N.301 Water bridges: A:R.303, A:S.305, A:R.306 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.18: 2 residues within 4Å: Chain A: K.475, Q.491 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.475 Salt bridges: A:K.475 PO4.19: 4 residues within 4Å: Chain A: A.798, Y.799, T.800, L.801 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.799 PO4.20: 3 residues within 4Å: Chain A: D.592, G.593, Y.594 No protein-ligand interaction detected (PLIP)

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

CL.9: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.24 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: W.71 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: K.475, N.485, F.488 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain A: E.549 Chain B: F.14, I.112, D.113 Ligand excluded by PLIP

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.21: 25 residues within 4Å: Chain A: R.129, I.167, R.169, T.173, M.174, G.175, G.176, D.207, E.208, S.209, L.210, I.211, E.215, M.240, G.241, I.242, H.243, T.244, Q.285, I.298, E.299, T.376 Ligands: MN.1, MN.2, PO4.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.173, A:M.174, A:G.175, A:G.176, A:E.208, A:L.210, A:E.215, A:G.241, A:T.244, A:Q.285, A:E.299 Water bridges: A:H.243, A:T.244 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.22: 19 residues within 4Å: Chain A: P.690, V.713, R.715, M.725, H.754, F.755, L.756, E.761, A.785, G.786, V.787, H.788, S.789, Q.829, I.840, E.841, P.909 Ligands: MN.6, K.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.715, A:R.715, A:H.754, A:L.756, A:E.761, A:G.786, A:S.789, A:S.789, A:E.841 Water bridges: A:H.788 Salt bridges: A:R.715, A:H.788

1 x ORN: L-ornithine(Non-covalent)

ORN.23: 11 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, V.893, L.895, L.907, H.1039, Y.1040, D.1041, T.1042 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.895 Hydrogen bonds: A:A.793, A:E.892, A:D.1041, A:T.1042 Water bridges: A:Y.1040

1 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.24: 7 residues within 4Å: Chain A: V.19, Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.19, A:Q.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis. Biochemistry (1998)

Release Date

1998-10-21

Peptides

CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN): A
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)

CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)

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