SMTL ID : 1c3o.1

CRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTANT C269S WITH BOUND GLUTAMINE

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, PO4.14, ADP.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.3 MN.2: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, K.11, PO4.14, ADP.15 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.3 MN.5: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: K.6, ADP.16 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, H2O.21 MN.23: 7 residues within 4Å: Chain C: M.174, E.299, N.301 Ligands: MN.24, K.26, PO4.36, ADP.40 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.39 MN.24: 7 residues within 4Å: Chain C: H.243, Q.285, E.299 Ligands: MN.23, K.33, PO4.36, ADP.40 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, H2O.39 MN.27: 3 residues within 4Å: Chain C: Q.829, E.841 Ligands: ADP.41 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.841, H2O.56, H2O.57 MN.46: 7 residues within 4Å: Chain E: M.174, E.299, N.301 Ligands: MN.47, K.49, PO4.58, ADP.60 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.76 MN.47: 7 residues within 4Å: Chain E: H.243, Q.285, E.299 Ligands: MN.46, K.56, PO4.58, ADP.60 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, H2O.76 MN.50: 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.94, H2O.94 MN.68: 7 residues within 4Å: Chain G: M.174, E.299, N.301 Ligands: MN.69, K.71, PO4.81, ADP.82 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.114 MN.69: 7 residues within 4Å: Chain G: H.243, Q.285, E.299 Ligands: MN.68, K.78, PO4.81, ADP.82 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, H2O.113 MN.72: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ADP.83 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.841

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: 7 residues within 4Å: Chain A: A.126, E.127, R.129, E.299, M.300, N.301 Ligands: MN.1 Ligand excluded by PLIP K.6: 4 residues within 4Å: Chain A: E.841, N.843 Ligands: MN.5, ADP.16 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.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 PLIP K.12: 3 residues within 4Å: Chain A: D.84, G.112, T.114 Ligand excluded by PLIP K.13: 3 residues within 4Å: Chain A: T.143, A.144, R.145 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.41 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.33: 6 residues within 4Å: Chain C: E.217, T.244, N.283, Q.285 Ligands: MN.24, PO4.36 Ligand excluded by PLIP K.34: 3 residues within 4Å: Chain C: D.84, G.112, T.114 Ligand excluded by PLIP K.35: 3 residues within 4Å: Chain C: T.143, A.144, R.145 Ligand excluded by PLIP K.43: 3 residues within 4Å: Chain C: R.490 Chain D: H.16, D.112 Ligand excluded by PLIP K.45: 2 residues within 4Å: Chain E: T.143, A.144 Ligand excluded by PLIP K.48: 6 residues within 4Å: Chain E: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.49: 6 residues within 4Å: Chain E: A.126, E.127, E.299, M.300, N.301 Ligands: MN.46 Ligand excluded by PLIP K.51: 3 residues within 4Å: Chain E: E.841, N.843 Ligands: ADP.61 Ligand excluded by PLIP K.52: 6 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.56: 6 residues within 4Å: Chain E: E.217, T.244, N.283, Q.285 Ligands: MN.47, PO4.58 Ligand excluded by PLIP K.57: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.66: 2 residues within 4Å: Chain F: H.16, D.112 Ligand excluded by PLIP K.70: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.71: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.68 Ligand excluded by PLIP K.73: 3 residues within 4Å: Chain G: E.841, N.843 Ligands: ADP.83 Ligand excluded by PLIP K.74: 6 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.78: 6 residues within 4Å: Chain G: E.217, T.244, N.283, Q.285 Ligands: MN.69, PO4.81 Ligand excluded by PLIP K.79: 3 residues within 4Å: Chain G: D.84, G.112, T.114 Ligand excluded by PLIP K.80: 2 residues within 4Å: Chain G: T.143, A.144 Ligand excluded by PLIP K.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 PLIP CL.9: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: E.549 Chain B: F.15, I.113, D.114 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: Q.93, T.173, M.174 Ligands: NET.39 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain C: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: E.549 Chain D: F.15, I.113, D.114 Ligand excluded by PLIP CL.53: 5 residues within 4Å: Chain E: Q.93, T.173, M.174, S.177 Ligands: NET.64 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain E: N.289, N.292, R.294 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain E: A.370, N.371, F.900, P.901, G.902 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.75: 4 residues within 4Å: Chain G: Q.93, T.173, M.174, S.177 Ligand excluded by PLIP CL.76: 3 residues within 4Å: Chain G: N.289, N.292, R.294 Ligand excluded by PLIP CL.77: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.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
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT

CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT

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