- 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)
- 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 PLIPK.4: 7 residues within 4Å:- Chain A: A.126, E.127, R.129, E.299, M.300, N.301
- Ligands: MN.1
Ligand excluded by PLIPK.6: 4 residues within 4Å:- Chain A: E.841, N.843
- Ligands: MN.5, ADP.16
Ligand excluded by PLIPK.7: 6 residues within 4Å:- Chain A: E.761, H.781, E.783, Q.784, V.787, S.792
Ligand excluded by PLIPK.11: 7 residues within 4Å:- Chain A: E.217, T.244, N.283, Q.285, S.307
- Ligands: MN.2, PO4.14
Ligand excluded by PLIPK.12: 3 residues within 4Å:- Chain A: D.84, G.112, T.114
Ligand excluded by PLIPK.13: 3 residues within 4Å:- Chain A: T.143, A.144, R.145
Ligand excluded by PLIPK.21: 2 residues within 4Å:- Chain B: H.16, D.112
Ligand excluded by PLIPK.25: 6 residues within 4Å:- Chain C: E.215, N.236, D.238, A.239, I.242, S.247
Ligand excluded by PLIPK.26: 6 residues within 4Å:- Chain C: A.126, E.127, E.299, M.300, N.301
- Ligands: MN.23
Ligand excluded by PLIPK.28: 3 residues within 4Å:- Chain C: E.841, N.843
- Ligands: ADP.41
Ligand excluded by PLIPK.29: 6 residues within 4Å:- Chain C: E.761, H.781, E.783, Q.784, V.787, S.792
Ligand excluded by PLIPK.33: 6 residues within 4Å:- Chain C: E.217, T.244, N.283, Q.285
- Ligands: MN.24, PO4.36
Ligand excluded by PLIPK.34: 3 residues within 4Å:- Chain C: D.84, G.112, T.114
Ligand excluded by PLIPK.35: 3 residues within 4Å:- Chain C: T.143, A.144, R.145
Ligand excluded by PLIPK.43: 3 residues within 4Å:- Chain C: R.490
- Chain D: H.16, D.112
Ligand excluded by PLIPK.45: 2 residues within 4Å:- Chain E: T.143, A.144
Ligand excluded by PLIPK.48: 6 residues within 4Å:- Chain E: E.215, N.236, D.238, A.239, I.242, S.247
Ligand excluded by PLIPK.49: 6 residues within 4Å:- Chain E: A.126, E.127, E.299, M.300, N.301
- Ligands: MN.46
Ligand excluded by PLIPK.51: 3 residues within 4Å:- Chain E: E.841, N.843
- Ligands: ADP.61
Ligand excluded by PLIPK.52: 6 residues within 4Å:- Chain E: E.761, H.781, E.783, Q.784, V.787, S.792
Ligand excluded by PLIPK.56: 6 residues within 4Å:- Chain E: E.217, T.244, N.283, Q.285
- Ligands: MN.47, PO4.58
Ligand excluded by PLIPK.57: 3 residues within 4Å:- Chain E: D.84, G.112, T.114
Ligand excluded by PLIPK.66: 2 residues within 4Å:- Chain F: H.16, D.112
Ligand excluded by PLIPK.70: 6 residues within 4Å:- Chain G: E.215, N.236, D.238, A.239, I.242, S.247
Ligand excluded by PLIPK.71: 6 residues within 4Å:- Chain G: A.126, E.127, E.299, M.300, N.301
- Ligands: MN.68
Ligand excluded by PLIPK.73: 3 residues within 4Å:- Chain G: E.841, N.843
- Ligands: ADP.83
Ligand excluded by PLIPK.74: 6 residues within 4Å:- Chain G: E.761, H.781, E.783, Q.784, V.787, S.792
Ligand excluded by PLIPK.78: 6 residues within 4Å:- Chain G: E.217, T.244, N.283, Q.285
- Ligands: MN.69, PO4.81
Ligand excluded by PLIPK.79: 3 residues within 4Å:- Chain G: D.84, G.112, T.114
Ligand excluded by PLIPK.80: 2 residues within 4Å:- Chain G: T.143, A.144
Ligand excluded by PLIPK.88: 2 residues within 4Å:- Chain H: H.16, D.112
Ligand excluded by PLIP- 16 x CL: CHLORIDE ION(Non-functional Binders)
CL.8: 4 residues within 4Å:- Chain A: Q.93, T.173, M.174
- Ligands: NET.19
Ligand excluded by PLIPCL.9: 3 residues within 4Å:- Chain A: N.289, N.292, R.294
Ligand excluded by PLIPCL.10: 5 residues within 4Å:- Chain A: A.370, N.371, F.900, P.901, G.902
Ligand excluded by PLIPCL.20: 4 residues within 4Å:- Chain A: E.549
- Chain B: F.15, I.113, D.114
Ligand excluded by PLIPCL.30: 4 residues within 4Å:- Chain C: Q.93, T.173, M.174
- Ligands: NET.39
Ligand excluded by PLIPCL.31: 4 residues within 4Å:- Chain C: W.213, N.289, N.292, R.294
Ligand excluded by PLIPCL.32: 5 residues within 4Å:- Chain C: A.370, N.371, F.900, P.901, G.902
Ligand excluded by PLIPCL.42: 4 residues within 4Å:- Chain C: E.549
- Chain D: F.15, I.113, D.114
Ligand excluded by PLIPCL.53: 5 residues within 4Å:- Chain E: Q.93, T.173, M.174, S.177
- Ligands: NET.64
Ligand excluded by PLIPCL.54: 3 residues within 4Å:- Chain E: N.289, N.292, R.294
Ligand excluded by PLIPCL.55: 5 residues within 4Å:- Chain E: A.370, N.371, F.900, P.901, G.902
Ligand excluded by PLIPCL.65: 4 residues within 4Å:- Chain E: E.549
- Chain F: F.15, I.113, D.114
Ligand excluded by PLIPCL.75: 4 residues within 4Å:- Chain G: Q.93, T.173, M.174, S.177
Ligand excluded by PLIPCL.76: 3 residues within 4Å:- Chain G: N.289, N.292, R.294
Ligand excluded by PLIPCL.77: 5 residues within 4Å:- Chain G: A.370, N.371, F.900, P.901, G.902
Ligand excluded by PLIPCL.87: 4 residues within 4Å:- Chain G: E.549
- Chain H: F.15, I.113, D.114
Ligand excluded by PLIP- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.14: 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.11, ADP.15
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
PO4.36: 12 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, K.33, ADP.40
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:G.175
- Water bridges: C:S.305, C:R.306, C:R.306
- Salt bridges: C:H.243, C:R.303, C:R.306
PO4.58: 12 residues within 4Å:- Chain E: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306
- Ligands: MN.46, MN.47, K.56, ADP.60
8 PLIP interactions:8 interactions with chain E- Hydrogen bonds: E:G.175, 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
PO4.59: 3 residues within 4Å:- Chain E: E.560, D.592, G.593
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:G.593
PO4.81: 12 residues within 4Å:- Chain G: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306
- Ligands: MN.68, MN.69, K.78, ADP.82
7 PLIP interactions:7 interactions with chain G- Hydrogen bonds: G:G.175
- Water bridges: 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.15: 26 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, N.301, T.376
- Ligands: MN.1, MN.2, PO4.14
16 PLIP interactions:16 interactions with chain A- Hydrogen bonds: 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
- Water bridges: A:R.129, A:R.129
- Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243
ADP.16: 18 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, E.841, P.909
- Ligands: MN.5, K.6
11 PLIP interactions:11 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
- Salt bridges: A:R.715, A:H.788
ADP.40: 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, PO4.36
17 PLIP interactions:17 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:T.244, C:Q.285
- Water bridges: C:R.129, C:T.173, C:H.243, C:T.244
- Salt bridges: C:R.129, C:R.129, C:R.169, C:H.243
ADP.41: 17 residues within 4Å:- Chain C: 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, I.840, E.841
- Ligands: MN.27, K.28
15 PLIP interactions:15 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:E.841
- Water bridges: C:Q.829, C:Q.829, C:Q.829, C:R.848, 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.46, MN.47, PO4.58
16 PLIP interactions:16 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:I.242, E:T.244, E:Q.285, E:Q.285
- Water bridges: E:R.129, E:R.129
- 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.50, K.51
11 PLIP interactions:11 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:S.789
- Salt bridges: E:R.715, E:H.788
ADP.82: 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.68, MN.69, PO4.81
15 PLIP interactions:15 interactions with chain G- Hydrogen bonds: G:G.175, G:G.176, G:E.208, G:L.210, G:E.215, G:G.241, G:I.242, G:T.244, G:Q.285
- Water bridges: G:T.173, G:T.173
- Salt bridges: G:R.129, G:R.129, G:R.169, G:H.243
ADP.83: 18 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, I.840, E.841, P.909
- Ligands: MN.72, K.73
12 PLIP interactions:12 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:V.787, G:S.789, G:S.789
- Water bridges: G:D.753
- Salt bridges: G:R.715, G:H.788
- 4 x ORN: L-ornithine(Non-covalent)
ORN.17: 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
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:L.895
- Hydrogen bonds: A:D.791, A:A.793, A:D.1041, A:D.1041, A:T.1042
- Water bridges: A:T.1043
ORN.37: 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, C:T.1043
- Water bridges: 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:E.783, E:A.793, E:D.1041, E:D.1041, E:T.1042
- Water bridges: E:T.1043
ORN.84: 10 residues within 4Å:- Chain G: 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 G- Hydrophobic interactions: G:L.895, G:L.907
- Hydrogen bonds: G:E.892, G:D.1041, G:T.1042
- Water bridges: G:Y.1040, G:T.1043
- 8 x GLN: GLUTAMINE(Non-covalent)
GLN.18: 7 residues within 4Å:- Chain A: R.528, A.537, T.538, E.552, N.554
- Chain B: R.120, R.123
10 PLIP interactions:5 interactions with chain A, 5 interactions with chain B,- Hydrogen bonds: A:T.538, A:T.538, A:E.552, A:N.554
- Water bridges: A:T.538, B:R.120, B:R.123, B:R.123
- Salt bridges: B:R.120, B:R.123
GLN.22: 13 residues within 4Å:- Chain B: S.47, N.240, G.241, P.242, G.243, S.269, L.270, Q.273, N.311, H.312, G.313, F.314, H.353
19 PLIP interactions:17 interactions with chain B, 2 Ligand-Ligand interactions- Hydrophobic interactions: B:L.270
- Hydrogen bonds: B:S.47, B:N.240, B:G.241, B:G.243, B:S.269, B:L.270, B:Q.273, B:N.311, B:G.313, B:F.314
- Water bridges: B:Q.51, B:Q.51, B:Q.51, B:G.241, B:H.291, B:N.311, Q.22, Q.22
GLN.38: 7 residues within 4Å:- Chain C: R.528, A.537, T.538, E.552, N.554
- Chain D: R.120, R.123
14 PLIP interactions:7 interactions with chain C, 6 interactions with chain D, 1 Ligand-Ligand interactions- Hydrogen bonds: C:T.538, C:T.538, C:E.552, C:N.554
- Water bridges: C:R.528, C:T.538, C:D.539, D:R.120, D:R.120, D:R.120, D:R.120, Q.38
- Salt bridges: D:R.120, D:R.123
GLN.44: 13 residues within 4Å:- Chain D: S.47, N.240, G.241, P.242, G.243, S.269, L.270, Q.273, N.311, H.312, G.313, F.314, H.353
17 PLIP interactions:2 Ligand-Ligand interactions, 15 interactions with chain D- Hydrogen bonds: Q.44, Q.44, D:S.47, D:N.240, D:G.241, D:G.243, D:S.269, D:L.270, D:Q.273, D:N.311, D:G.313, D:F.314
- Hydrophobic interactions: D:L.270, D:H.312
- Water bridges: D:Q.51, D:N.311, D:N.311
GLN.63: 8 residues within 4Å:- Chain E: R.528, A.537, T.538, D.539, E.552, N.554
- Chain F: R.120, R.123
12 PLIP interactions:6 interactions with chain E, 5 interactions with chain F, 1 Ligand-Ligand interactions- Hydrogen bonds: E:T.538, E:D.539, E:E.552, E:N.554
- Water bridges: E:R.528, E:D.539, F:R.123, F:R.123, F:R.123, Q.63
- Salt bridges: F:R.120, F:R.123
GLN.67: 14 residues within 4Å:- Chain F: S.47, N.240, G.241, P.242, G.243, I.268, S.269, L.270, Q.273, N.311, H.312, G.313, F.314, H.353
13 PLIP interactions:13 interactions with chain F,- Hydrophobic interactions: F:L.270, F:H.312
- Hydrogen bonds: F:S.47, F:G.241, F:G.243, F:S.269, F:L.270, F:Q.273, F:Q.273, F:G.313, F:F.314, F:H.353
- Water bridges: F:G.243
GLN.85: 8 residues within 4Å:- Chain G: R.528, A.537, T.538, D.539, E.552, N.554
- Chain H: R.120, R.123
9 PLIP interactions:5 interactions with chain G, 4 interactions with chain H- Hydrogen bonds: G:T.538, G:D.539, G:E.552, G:N.554
- Water bridges: G:R.343, H:R.120, H:R.123
- Salt bridges: H:R.120, H:R.123
GLN.89: 13 residues within 4Å:- Chain H: S.47, N.240, G.241, P.242, G.243, S.269, L.270, Q.273, N.311, H.312, G.313, F.314, H.353
12 PLIP interactions:12 interactions with chain H,- Hydrophobic interactions: H:L.270
- Hydrogen bonds: H:S.47, H:G.241, H:G.241, H:S.269, H:L.270, H:Q.273, H:Q.273, H:N.311, H:G.313, H:F.314
- Water bridges: H:G.243
- 4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)
NET.19: 6 residues within 4Å:- Chain A: Q.22, Q.93, T.94, N.97, N.936
- Ligands: CL.8
No protein-ligand interaction detected (PLIP)NET.39: 7 residues within 4Å:- Chain C: V.19, Q.22, Q.93, T.94, N.97, N.936
- Ligands: CL.30
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.19
NET.64: 6 residues within 4Å:- Chain E: Q.22, Q.93, T.94, N.97, N.936
- Ligands: CL.53
No protein-ligand interaction detected (PLIP)NET.86: 6 residues within 4Å:- Chain G: V.19, Q.22, Q.93, T.94, N.97, N.936
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., 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: ACEG
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT: BDFH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
EG
GB
BD
DF
FH
H
- 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)
- 32 x K: POTASSIUM ION(Non-covalent)
- 16 x CL: CHLORIDE ION(Non-functional Binders)
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
- 8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x ORN: L-ornithine(Non-covalent)
- 8 x GLN: GLUTAMINE(Non-covalent)
- 4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)
- 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: ACEG
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT: BDFH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
EG
GB
BD
DF
FH
H