SMTL ID : 1a9x.1 (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-4-4-mer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: K.475, Q.491 Ligands: CL.17 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.475, A:Q.491, A:Q.491, A:Q.491 Salt bridges: A:K.475 PO4.2: 4 residues within 4Å: Chain A: A.798, Y.799, T.800, L.801 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.799 Water bridges: A:Q.803 PO4.3: 3 residues within 4Å: Chain A: E.560, D.592, G.593 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.594 PO4.8: 12 residues within 4Å: Chain A: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.4, MN.5, K.19, ADP.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.175, A:N.301, A:N.301 Water bridges: A:R.306, A:R.306 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.31: 12 residues within 4Å: Chain C: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.27, MN.28, K.42, ADP.47 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.175, C:N.301 Water bridges: C:R.303, C:S.305 Salt bridges: C:H.243, C:R.303, C:R.306 PO4.44: 3 residues within 4Å: Chain C: D.518, Q.519, D.521 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.518, C:Q.519 PO4.45: 3 residues within 4Å: Chain C: D.592, G.593, Y.594 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.592, C:Y.594 PO4.46: 3 residues within 4Å: Chain C: Y.799, T.800, L.801 3 PLIP interactions: 3 interactions with chain C Water bridges: C:L.801, C:L.801, C:Q.803 PO4.57: 12 residues within 4Å: Chain E: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.53, MN.54, K.68, ADP.72 9 PLIP interactions: 9 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 Salt bridges: E:H.243, E:R.303, E:R.306 PO4.70: 4 residues within 4Å: Chain E: A.798, Y.799, T.800, L.801 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.799 Water bridges: E:A.798, E:Q.806 PO4.71: 3 residues within 4Å: Chain E: E.560, G.593, Y.594 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.560 PO4.82: 12 residues within 4Å: Chain G: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.78, MN.79, K.93, ADP.98 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.175, G:N.301 Water bridges: G:R.303, G:S.305, G:R.306 Salt bridges: G:H.243, G:R.303, G:R.306 PO4.95: 2 residues within 4Å: Chain G: K.475, Q.491 2 PLIP interactions: 2 interactions with chain G Water bridges: G:K.475 Salt bridges: G:K.475 PO4.96: 4 residues within 4Å: Chain G: A.798, Y.799, T.800, L.801 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.799 PO4.97: 3 residues within 4Å: Chain G: D.592, G.593, Y.594 No protein-ligand interaction detected (PLIP)

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

MN.4: 7 residues within 4Å: Chain A: M.174, E.299, N.301 Ligands: MN.5, K.7, PO4.8, ADP.21 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.27 MN.5: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.4, PO4.8, K.19, ADP.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.299 MN.9: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: K.10, ADP.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.841 MN.27: 7 residues within 4Å: Chain C: M.174, E.299, N.301 Ligands: MN.28, K.30, PO4.31, ADP.47 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.63 MN.28: 7 residues within 4Å: Chain C: H.243, Q.285, E.299 Ligands: MN.27, PO4.31, K.42, ADP.47 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, H2O.71 MN.32: 3 residues within 4Å: Chain C: Q.829, E.841 Ligands: ADP.48 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.841, H2O.78 MN.53: 7 residues within 4Å: Chain E: M.174, E.299, N.301 Ligands: MN.54, K.56, PO4.57, ADP.72 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.120 MN.54: 6 residues within 4Å: Chain E: Q.285, E.299 Ligands: MN.53, PO4.57, K.68, ADP.72 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, H2O.120 MN.58: 3 residues within 4Å: Chain E: Q.829, E.841 Ligands: ADP.73 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.841 MN.78: 7 residues within 4Å: Chain G: M.174, E.299, N.301 Ligands: MN.79, K.81, PO4.82, ADP.98 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.162 MN.79: 7 residues within 4Å: Chain G: H.243, Q.285, E.299 Ligands: MN.78, PO4.82, K.93, ADP.98 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, H2O.163 MN.83: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ADP.99 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.841

32 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain A: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.7: 7 residues within 4Å: Chain A: A.126, E.127, R.129, E.299, M.300, N.301 Ligands: MN.4 Ligand excluded by PLIP K.10: 4 residues within 4Å: Chain A: E.841, N.843 Ligands: MN.9, ADP.22 Ligand excluded by PLIP K.11: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.18: 3 residues within 4Å: Chain A: D.84, G.112, T.114 Ligand excluded by PLIP K.19: 7 residues within 4Å: Chain A: E.217, T.244, N.283, Q.285, S.307 Ligands: MN.5, PO4.8 Ligand excluded by PLIP K.20: 3 residues within 4Å: Chain A: T.143, A.144, R.145 Ligand excluded by PLIP K.26: 2 residues within 4Å: Chain B: H.15, D.111 Ligand excluded by PLIP K.29: 6 residues within 4Å: Chain C: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.30: 6 residues within 4Å: Chain C: A.126, E.127, E.299, M.300, N.301 Ligands: MN.27 Ligand excluded by PLIP K.33: 3 residues within 4Å: Chain C: E.841, N.843 Ligands: ADP.48 Ligand excluded by PLIP K.34: 7 residues within 4Å: Chain C: E.761, H.781, E.783, Q.784, A.785, V.787, S.792 Ligand excluded by PLIP K.41: 3 residues within 4Å: Chain C: D.84, G.112, T.114 Ligand excluded by PLIP K.42: 7 residues within 4Å: Chain C: E.217, T.244, N.283, Q.285, N.301 Ligands: MN.28, PO4.31 Ligand excluded by PLIP K.43: 3 residues within 4Å: Chain C: T.143, A.144, R.145 Ligand excluded by PLIP K.52: 2 residues within 4Å: Chain D: H.15, D.111 Ligand excluded by PLIP K.55: 6 residues within 4Å: Chain E: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.56: 6 residues within 4Å: Chain E: A.126, E.127, E.299, M.300, N.301 Ligands: MN.53 Ligand excluded by PLIP K.59: 3 residues within 4Å: Chain E: E.841, N.843 Ligands: ADP.73 Ligand excluded by PLIP K.60: 6 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.67: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.68: 6 residues within 4Å: Chain E: E.217, T.244, N.283, Q.285 Ligands: MN.54, PO4.57 Ligand excluded by PLIP K.69: 2 residues within 4Å: Chain E: T.143, A.144 Ligand excluded by PLIP K.77: 2 residues within 4Å: Chain F: H.15, D.111 Ligand excluded by PLIP K.80: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.81: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.78 Ligand excluded by PLIP K.84: 3 residues within 4Å: Chain G: E.841, N.843 Ligands: ADP.99 Ligand excluded by PLIP K.85: 6 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.92: 3 residues within 4Å: Chain G: D.84, G.112, T.114 Ligand excluded by PLIP K.93: 7 residues within 4Å: Chain G: E.217, T.244, N.283, Q.285, S.307 Ligands: MN.79, PO4.82 Ligand excluded by PLIP K.94: 3 residues within 4Å: Chain G: T.143, A.144, R.145 Ligand excluded by PLIP K.103: 2 residues within 4Å: Chain H: H.15, D.111 Ligand excluded by PLIP

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

CL.12: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.24 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: W.71 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: K.475, N.485, F.488 Ligands: PO4.1 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 CL.35: 5 residues within 4Å: Chain C: Q.93, T.173, M.174, S.177 Ligands: NET.50 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain C: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain C: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain C: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: H.70, W.71 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: K.475, N.485, F.488 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain C: E.549 Chain D: F.14, I.112, D.113 Ligand excluded by PLIP CL.61: 5 residues within 4Å: Chain E: Q.93, T.173, M.174, S.177 Ligands: NET.75 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain E: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.63: 5 residues within 4Å: Chain E: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain E: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain E: W.71 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain E: K.475, N.485, F.488 Ligand excluded by PLIP CL.76: 4 residues within 4Å: Chain E: E.549 Chain F: F.14, I.112, D.113 Ligand excluded by PLIP CL.86: 5 residues within 4Å: Chain G: Q.93, T.173, M.174, S.177 Ligands: NET.101 Ligand excluded by PLIP CL.87: 4 residues within 4Å: Chain G: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.88: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.89: 4 residues within 4Å: Chain G: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.90: 1 residues within 4Å: Chain G: W.71 Ligand excluded by PLIP CL.91: 3 residues within 4Å: Chain G: K.475, N.485, F.488 Ligand excluded by PLIP CL.102: 4 residues within 4Å: Chain G: E.549 Chain H: F.14, I.112, D.113 Ligand excluded by PLIP

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

ADP.21: 26 residues within 4Å: Chain A: R.129, A.144, 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.4, MN.5, PO4.8 16 PLIP interactions: 16 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:I.242, A:T.244, A:Q.285, A:Q.285, A:E.299 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.9, K.10 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.715, A:H.754, A:L.756, A:E.761, A:G.786, A:S.789, A:S.789 Water bridges: A:R.715, A:R.715 Salt bridges: A:R.715, A:H.788 ADP.47: 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.27, MN.28, PO4.31 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:T.173, C:G.175, C:G.176, C:E.208, C:L.210, C:E.215, C:G.241, C:I.242, C:T.244, C:Q.285, C:E.299 Water bridges: C:R.129, C:R.129, C:H.243, C:Q.285 Salt bridges: C:R.129, C:R.129, C:R.169, C:H.243 ADP.48: 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.32, K.33 16 PLIP interactions: 16 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:V.787, C:S.789, C:Q.829, C:E.841 Water bridges: C:H.788, C:Q.829, C:N.843, C:R.848 Salt bridges: C:R.715, C:H.788 ADP.72: 25 residues within 4Å: Chain E: 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.53, MN.54, PO4.57 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.175, E:G.176, E:E.208, E:L.210, E:E.215, E:G.241, E:T.244, E:T.244, E:Q.285 Salt bridges: E:R.129, E:R.129, E:R.169, E:H.243 ADP.73: 18 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, E.841, P.909 Ligands: MN.58, K.59 10 PLIP interactions: 10 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 Salt bridges: E:R.715, E:H.788 ADP.98: 25 residues within 4Å: Chain G: 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.78, MN.79, PO4.82 15 PLIP interactions: 15 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:Q.285, G:E.299 Salt bridges: G:R.129, G:R.129, G:R.169, G:H.243 ADP.99: 19 residues within 4Å: Chain G: 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.83, K.84 10 PLIP interactions: 10 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 Salt bridges: G:R.715, G:H.788

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

ORN.23: 9 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, V.893, L.907, Y.1040, D.1041, T.1042 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.791, A:A.793, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:P.905, A:Y.1040, A:Y.1040, A:T.1043 ORN.49: 11 residues within 4Å: Chain C: E.783, D.791, S.792, A.793, E.892, V.893, L.895, L.907, Y.1040, D.1041, T.1042 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.895, C:L.907 Hydrogen bonds: C:D.791, C:A.793, C:D.1041, C:T.1042 Water bridges: C:E.783, C:Y.1040 ORN.74: 11 residues within 4Å: Chain E: E.783, D.791, A.793, E.892, V.893, L.895, L.907, H.1039, Y.1040, D.1041, T.1042 9 PLIP interactions: 9 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, E:T.1043 Water bridges: E:H.1039, E:Y.1040 ORN.100: 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:Y.1040

4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.24: 5 residues within 4Å: Chain A: Q.22, T.94, N.97, N.936 Ligands: CL.12 No protein-ligand interaction detected (PLIP) NET.50: 6 residues within 4Å: Chain C: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.35 No protein-ligand interaction detected (PLIP) NET.75: 5 residues within 4Å: Chain E: Q.22, T.94, N.97, N.936 Ligands: CL.61 No protein-ligand interaction detected (PLIP) NET.101: 7 residues within 4Å: Chain G: V.19, Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.86 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.19, G: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): 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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