SMTL ID : 1cs0.5 (4 other biounits)

Crystal structure of carbamoyl phosphate synthetase complexed at CYS269 in the small subunit with the tetrahedral mimic l-glutamate gamma-semialdehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.22 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.940, K.941 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.950, E.951, G.952, S.1018 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: V.284, K.285 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain A: E.549 Chain B: F.15, I.113, D.114 Ligand excluded by PLIP

9 x K: POTASSIUM ION(Non-covalent)

K.6: 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.7: 6 residues within 4Å: Chain A: E.217, T.244, N.283, Q.285 Ligands: MN.11, PO4.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.217 K.8: 1 residues within 4Å: Chain A: T.279 No protein-ligand interaction detected (PLIP) K.9: 2 residues within 4Å: Chain A: T.143, A.144 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.143, A:A.144 K.12: 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.13: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:E.299, A:M.300, H2O.7, H2O.25 K.15: 3 residues within 4Å: Chain A: E.841, N.843 Ligands: ADP.20 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.841 K.16: 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.25: 2 residues within 4Å: Chain B: H.16, D.112 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.16, B:D.112, H2O.17, H2O.35

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

MN.10: 7 residues within 4Å: Chain A: M.174, E.299, N.301 Ligands: MN.11, K.13, PO4.17, ADP.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.3 MN.11: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: K.7, MN.10, PO4.17, ADP.19 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.3 MN.14: 3 residues within 4Å: Chain A: Q.829, E.841 Ligands: ADP.20 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, H2O.3

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

PO4.17: 12 residues within 4Å: Chain A: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: K.7, MN.10, MN.11, ADP.19 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.175, A:E.299, A:N.301 Water bridges: A:Q.285, A:R.303, A:S.305, A:R.306 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.18: 5 residues within 4Å: Chain A: P.797, P.885, P.886, Y.887, Y.888 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.885 Water bridges: A:Y.888

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

ADP.19: 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.10, MN.11, PO4.17 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.173, A:T.173, 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, A:E.299 Water bridges: A:R.129, A:R.129, A:H.243, A:Q.285 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.20: 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.14, K.15 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:Q.829 Salt bridges: A:R.715, A:H.788

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

ORN.21: 9 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, V.893, L.907, Y.1040, D.1041, T.1042 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.783, A:A.793, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:L.907, A:Y.1040, A:T.1043

1 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.22: 6 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway. Biochemistry (1999)

Release Date

1999-12-10

Peptides

CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT: A
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT

CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT

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