SMTL ID : 1kee.1 (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-4-4-mer

Ligands

12 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 MN.23: 7 residues within 4Å: Chain C: M.174, E.299, N.301 Ligands: MN.24, K.26, PO4.38, ADP.39 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.46 MN.24: 6 residues within 4Å: Chain C: H.243, Q.285, E.299 Ligands: MN.23, PO4.38, ADP.39 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, H2O.48 MN.27: 3 residues within 4Å: Chain C: Q.829, E.841 Ligands: ADP.40 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.841, H2O.60, H2O.60 MN.45: 7 residues within 4Å: Chain E: M.174, E.299, N.301 Ligands: MN.46, K.48, PO4.59, ADP.60 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.88 MN.46: 5 residues within 4Å: Chain E: Q.285, E.299 Ligands: MN.45, PO4.59, ADP.60 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, H2O.90 MN.49: 3 residues within 4Å: Chain E: Q.829, E.841 Ligands: ADP.61 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.841, H2O.102, H2O.102 MN.66: 7 residues within 4Å: Chain G: M.174, E.299, N.301 Ligands: MN.67, K.69, PO4.80, ADP.81 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.132 MN.67: 6 residues within 4Å: Chain G: H.243, Q.285, E.299 Ligands: MN.66, PO4.80, ADP.81 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, H2O.134 MN.70: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ADP.82 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.841, H2O.146, H2O.146

32 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 Ligand excluded by PLIP K.4: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.1 Ligand excluded by PLIP K.6: 5 residues within 4Å: Chain A: E.841, N.843, R.845 Ligands: MN.5, ADP.18 Ligand excluded by PLIP K.7: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.8: 3 residues within 4Å: Chain A: T.143, A.144, R.145 Ligand excluded by PLIP K.9: 5 residues within 4Å: Chain A: G.382, E.383, N.570, N.602, E.604 Ligand excluded by PLIP K.10: 3 residues within 4Å: Chain A: D.84, G.112, T.114 Ligand excluded by PLIP K.21: 2 residues within 4Å: Chain B: H.16, D.112 Ligand excluded by PLIP K.25: 6 residues within 4Å: Chain C: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.26: 6 residues within 4Å: Chain C: A.126, E.127, E.299, M.300, N.301 Ligands: MN.23 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain C: E.841, N.843 Ligands: ADP.40 Ligand excluded by PLIP K.29: 6 residues within 4Å: Chain C: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.30: 3 residues within 4Å: Chain C: T.143, A.144, R.145 Ligand excluded by PLIP K.31: 6 residues within 4Å: Chain C: G.382, E.383, P.569, N.570, N.602, E.604 Ligand excluded by PLIP K.32: 3 residues within 4Å: Chain C: D.84, G.112, T.114 Ligand excluded by PLIP K.43: 2 residues within 4Å: Chain D: H.16, D.112 Ligand excluded by PLIP K.47: 6 residues within 4Å: Chain E: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.48: 6 residues within 4Å: Chain E: A.126, E.127, E.299, M.300, N.301 Ligands: MN.45 Ligand excluded by PLIP K.50: 3 residues within 4Å: Chain E: E.841, N.843 Ligands: ADP.61 Ligand excluded by PLIP K.51: 6 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.52: 3 residues within 4Å: Chain E: T.143, A.144, R.145 Ligand excluded by PLIP K.53: 6 residues within 4Å: Chain E: G.382, E.383, P.569, N.570, N.602, E.604 Ligand excluded by PLIP K.54: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.64: 2 residues within 4Å: Chain F: H.16, D.112 Ligand excluded by PLIP K.68: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.69: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.66 Ligand excluded by PLIP K.71: 3 residues within 4Å: Chain G: E.841, N.843 Ligands: ADP.82 Ligand excluded by PLIP K.72: 6 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.73: 2 residues within 4Å: Chain G: T.143, A.144 Ligand excluded by PLIP K.74: 6 residues within 4Å: Chain G: G.382, E.383, P.569, N.570, N.602, E.604 Ligand excluded by PLIP K.75: 3 residues within 4Å: Chain G: D.84, G.112, T.114 Ligand excluded by PLIP K.85: 2 residues within 4Å: Chain H: H.16, D.112 Ligand excluded by PLIP

22 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 CL.33: 4 residues within 4Å: Chain C: Q.93, T.173, M.174 Ligands: NET.42 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain C: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain C: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: K.475, N.485, F.488 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain C: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain C: E.549 Chain D: F.15, I.113, D.114 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain E: Q.93, T.173, M.174, S.177 Ligands: NET.63 Ligand excluded by PLIP CL.56: 4 residues within 4Å: Chain E: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.57: 5 residues within 4Å: Chain E: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain E: K.475, N.485, F.488 Ligand excluded by PLIP CL.65: 4 residues within 4Å: Chain E: E.549 Chain F: F.15, I.113, D.114 Ligand excluded by PLIP CL.76: 5 residues within 4Å: Chain G: Q.93, T.173, M.174, S.177 Ligands: NET.84 Ligand excluded by PLIP CL.77: 3 residues within 4Å: Chain G: N.289, N.292, R.294 Ligand excluded by PLIP CL.78: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain G: K.475, N.485, F.488 Ligand excluded by PLIP CL.86: 4 residues within 4Å: Chain G: E.549 Chain H: F.15, I.113, D.114 Ligand excluded by PLIP

4 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:N.301, 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 PO4.38: 11 residues within 4Å: Chain C: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.23, MN.24, ADP.39 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.175, C:N.301 Water bridges: C:T.244, C:T.244, C:R.303, C:R.306, C:R.306 Salt bridges: C:H.243, C:R.303, C:R.306 PO4.59: 11 residues within 4Å: Chain E: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.45, MN.46, ADP.60 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.175, E:N.301, E:N.301 Water bridges: E:Q.285, E:R.303, E:S.305, E:R.306 Salt bridges: E:H.243, E:R.303, E:R.306 PO4.80: 11 residues within 4Å: Chain G: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.66, MN.67, ADP.81 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.175, G:N.301 Water bridges: G:T.244, G:R.303, G:S.305, G:R.306 Salt bridges: G:H.243, G:R.303, G:R.306

8 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 17 PLIP interactions: 17 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:Q.285, A:E.299 Water bridges: A:R.129, A:R.129 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 13 PLIP interactions: 13 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 Water bridges: A:Q.829, A:Q.829, A:N.843, A:R.848 Salt bridges: A:R.715, A:H.788 ADP.39: 25 residues within 4Å: Chain C: 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.23, MN.24, PO4.38 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.175, C:G.176, C:E.208, C:L.210, C:E.215, C:G.241, C:T.244, C:Q.285, C:Q.285, C:E.299 Water bridges: C:R.129, C:T.173 Salt bridges: C:R.129, C:R.129, C:R.169, C:H.243 ADP.40: 19 residues within 4Å: Chain C: 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.27, K.28 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.715, C:R.715, C:H.754, C:L.756, C:E.761, C:G.786, C:S.789, C:S.789 Water bridges: C:R.848 Salt bridges: C:R.715, C:H.788 ADP.60: 24 residues within 4Å: Chain E: R.129, I.167, R.169, T.173, M.174, G.175, G.176, 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.45, MN.46, PO4.59 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:M.174, E:G.175, E:G.176, E:E.208, E:L.210, E:E.215, E:G.241, E:I.242, E:T.244, E:Q.285, E:Q.285, E:E.299 Salt bridges: E:R.129, E:R.129, E:R.169, E:H.243 ADP.61: 19 residues within 4Å: Chain E: 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.49, K.50 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:R.715, E:R.715, E:H.754, E:L.756, E:E.761, E:G.786, E:S.789, E:S.789 Water bridges: E:E.841, E:N.843, E:N.843, E:R.848 Salt bridges: E:R.715, E:H.788 ADP.81: 24 residues within 4Å: Chain G: R.129, I.167, R.169, T.173, M.174, G.175, G.176, 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.66, MN.67, PO4.80 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:M.174, G:G.175, G:G.176, G:E.208, G:L.210, G:E.215, G:G.241, G:T.244, G:Q.285, G:E.299 Salt bridges: G:R.129, G:R.129, G:R.169, G:H.243 ADP.82: 17 residues within 4Å: Chain G: P.690, R.715, M.725, H.754, F.755, L.756, E.761, A.785, G.786, V.787, H.788, S.789, Q.829, E.841, P.909 Ligands: MN.70, K.71 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:R.715, G:R.715, G:H.754, G:L.756, G:E.761, G:G.786, G:S.789, G:S.789 Water bridges: G:D.753, G:Q.829, G:E.841, G:N.843, G:R.848 Salt bridges: G:R.715, G:H.788

4 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 ORN.41: 10 residues within 4Å: Chain C: E.783, D.791, A.793, E.892, V.893, L.895, L.907, Y.1040, D.1041, T.1042 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.895 Hydrogen bonds: C:D.791, C:A.793, C:D.1041, C:T.1042 Water bridges: C:E.783, C:Y.1040 ORN.62: 10 residues within 4Å: Chain E: E.783, D.791, A.793, E.892, V.893, L.895, L.907, Y.1040, D.1041, T.1042 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.895 Hydrogen bonds: E:D.791, E:A.793, E:D.1041, E:D.1041, E:T.1042 Water bridges: E:T.1043 ORN.83: 11 residues within 4Å: Chain G: 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 G Hydrophobic interactions: G:L.895 Hydrogen bonds: G:A.793, G:E.892, G:D.1041, G:T.1042 Water bridges: G:T.1043

4 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 NET.42: 6 residues within 4Å: Chain C: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.33 No protein-ligand interaction detected (PLIP) NET.63: 6 residues within 4Å: Chain E: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.55 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.93 NET.84: 6 residues within 4Å: Chain G: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.76 No protein-ligand interaction detected (PLIP)

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: ACEG
Carbamoyl-phosphate synthetase small chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Carbamoyl-phosphate synthetase large chain

Carbamoyl-phosphate synthetase small chain

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