SMTL ID : 1kee.4 (4 other biounits)

Inactivation of the Amidotransferase Activity of Carbamoyl Phosphate Synthetase by the Antibiotic Acivicin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, PO4.16, ADP.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.5 MN.2: 6 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, PO4.16, ADP.17 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.7 MN.5: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: K.6, ADP.18 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.841, H2O.19, H2O.19

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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.127, A:E.299, A:M.300, H2O.5 K.6: 5 residues within 4Å: Chain A: E.841, N.843, R.845 Ligands: MN.5, ADP.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.841, A:E.841 K.7: 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.8: 3 residues within 4Å: Chain A: T.143, A.144, R.145 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.143, H2O.5 K.9: 5 residues within 4Å: Chain A: G.382, E.383, N.570, N.602, E.604 No protein-ligand interaction detected (PLIP) K.10: 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.1 K.21: 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.16, H2O.35

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

CL.11: 4 residues within 4Å: Chain A: Q.93, T.173, M.174 Ligands: NET.20 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: K.475, N.485, F.488 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: E.549 Chain B: F.15, I.113, D.114 Ligand excluded by PLIP

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

PO4.16: 11 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, ADP.17 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.175, A:E.299, A:N.301 Water bridges: A:Q.285, A:R.303, A:R.306 Salt bridges: A:H.243, A:R.303, A:R.306

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

ADP.17: 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, PO4.16 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: 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, A:N.301 Water bridges: A:R.129, A:R.129, A:H.243, A:T.244 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.18: 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.5, K.6 16 PLIP interactions: 16 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:E.841 Water bridges: A:H.788, A:H.788, A:Q.829, A:Q.829, A:N.843, A:R.848 Salt bridges: A:R.715, A:H.788

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

ORN.19: 10 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, V.893, L.895, L.907, Y.1040, D.1041, T.1042 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.895 Hydrogen bonds: A:D.791, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:T.1043

1 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.20: 6 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, B.W. et al., Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin. J.Biol.Chem. (2002)

Release Date

2001-12-21

Peptides

Carbamoyl-phosphate synthetase large chain: A
Carbamoyl-phosphate synthetase small chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carbamoyl-phosphate synthetase large chain

Carbamoyl-phosphate synthetase small chain

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