SMTL ID : 1ce8.1 (4 other biounits)

CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEXED WITH THE ALLOSTERIC LIGAND IMP

Coordinates

PDB Format Compare

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, PO4.13, ADP.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.24 MN.2: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, K.5, PO4.13, ADP.14 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.23 MN.6: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: K.7, ADP.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.841 MN.21: 7 residues within 4Å: Chain C: M.174, E.299, N.301 Ligands: MN.22, K.24, PO4.33, ADP.34 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.64 MN.22: 7 residues within 4Å: Chain C: H.243, Q.285, E.299 Ligands: MN.21, K.25, PO4.33, ADP.34 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, H2O.63 MN.26: 3 residues within 4Å: Chain C: Q.829, E.841 Ligands: ADP.35 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.841 MN.41: 7 residues within 4Å: Chain E: M.174, E.299, N.301 Ligands: MN.42, K.44, PO4.53, ADP.54 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.100 MN.42: 7 residues within 4Å: Chain E: H.243, Q.285, E.299 Ligands: MN.41, K.45, PO4.53, ADP.54 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, H2O.100 MN.46: 4 residues within 4Å: Chain E: S.789, Q.829, E.841 Ligands: ADP.55 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.841 MN.61: 7 residues within 4Å: Chain G: M.174, E.299, N.301 Ligands: MN.62, K.64, PO4.73, ADP.74 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.145 MN.62: 7 residues within 4Å: Chain G: H.243, Q.285, E.299 Ligands: MN.61, K.65, PO4.73, ADP.74 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, H2O.145 MN.66: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ADP.75 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.841

28 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.5: 6 residues within 4Å: Chain A: E.217, T.244, N.283, Q.285 Ligands: MN.2, PO4.13 Ligand excluded by PLIP K.7: 4 residues within 4Å: Chain A: E.841, N.843 Ligands: MN.6, ADP.15 Ligand excluded by PLIP K.8: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.9: 3 residues within 4Å: Chain A: D.84, G.112, T.114 Ligand excluded by PLIP K.20: 2 residues within 4Å: Chain B: H.16, D.112 Ligand excluded by PLIP K.23: 6 residues within 4Å: Chain C: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.24: 6 residues within 4Å: Chain C: A.126, E.127, E.299, M.300, N.301 Ligands: MN.21 Ligand excluded by PLIP K.25: 6 residues within 4Å: Chain C: E.217, T.244, N.283, Q.285 Ligands: MN.22, PO4.33 Ligand excluded by PLIP K.27: 3 residues within 4Å: Chain C: E.841, N.843 Ligands: ADP.35 Ligand excluded by PLIP K.28: 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.29: 3 residues within 4Å: Chain C: D.84, G.112, T.114 Ligand excluded by PLIP K.40: 2 residues within 4Å: Chain D: H.16, D.112 Ligand excluded by PLIP K.43: 6 residues within 4Å: Chain E: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.44: 6 residues within 4Å: Chain E: A.126, E.127, E.299, M.300, N.301 Ligands: MN.41 Ligand excluded by PLIP K.45: 6 residues within 4Å: Chain E: E.217, T.244, N.283, Q.285 Ligands: MN.42, PO4.53 Ligand excluded by PLIP K.47: 3 residues within 4Å: Chain E: E.841, N.843 Ligands: ADP.55 Ligand excluded by PLIP K.48: 6 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.49: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.60: 2 residues within 4Å: Chain F: H.16, D.112 Ligand excluded by PLIP K.63: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.64: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.61 Ligand excluded by PLIP K.65: 7 residues within 4Å: Chain G: E.217, T.244, N.283, Q.285, N.301 Ligands: MN.62, PO4.73 Ligand excluded by PLIP K.67: 3 residues within 4Å: Chain G: E.841, N.843 Ligands: ADP.75 Ligand excluded by PLIP K.68: 7 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, A.785, V.787, S.792 Ligand excluded by PLIP K.69: 3 residues within 4Å: Chain G: D.84, G.112, T.114 Ligand excluded by PLIP K.80: 2 residues within 4Å: Chain H: H.16, D.112 Ligand excluded by PLIP

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

CL.10: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.18 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: Q.93, T.173, M.174 Ligands: NET.38 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.50: 5 residues within 4Å: Chain E: Q.93, T.173, M.174, S.177 Ligands: NET.58 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain E: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.52: 5 residues within 4Å: Chain E: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.70: 5 residues within 4Å: Chain G: Q.93, T.173, M.174, S.177 Ligands: NET.78 Ligand excluded by PLIP CL.71: 3 residues within 4Å: Chain G: N.289, N.292, R.294 Ligand excluded by PLIP CL.72: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP

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

PO4.13: 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.5, ADP.14 10 PLIP interactions: 10 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.303, A:S.305 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.33: 12 residues within 4Å: Chain C: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.21, MN.22, K.25, ADP.34 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.175, C:E.299, C:N.301 Water bridges: C:Q.285, C:R.303, C:S.305, C:R.306 Salt bridges: C:H.243, C:R.303, C:R.306 PO4.53: 12 residues within 4Å: Chain E: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.41, MN.42, K.45, ADP.54 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.175, E:Q.285, 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 PO4.73: 12 residues within 4Å: Chain G: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.61, MN.62, K.65, ADP.74 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.175, G:T.244, G:E.299, G:N.301 Water bridges: G:Q.285, 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.14: 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, PO4.13 15 PLIP interactions: 15 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 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.15: 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.6, K.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.715, A:H.754, A:L.756, A:E.761, A:G.786, A:V.787, A:S.789 Salt bridges: A:R.715, A:H.788 ADP.34: 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.21, MN.22, PO4.33 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.173, C:M.174, 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:E.299 Water bridges: C:R.129, C:T.173, C:Q.285 Salt bridges: C:R.129, C:R.129, C:R.169, C:H.243 ADP.35: 18 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, P.909 Ligands: MN.26, K.27 10 PLIP interactions: 10 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 Salt bridges: C:R.715, C:H.788 ADP.54: 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.41, MN.42, PO4.53 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:T.173, E:G.175, E:G.176, E:E.208, E:L.210, E:E.215, E:G.241, E:T.244, E:Q.285 Water bridges: E:R.129, E:R.129, E:H.243, E:Q.285 Salt bridges: E:R.129, E:R.129, E:R.169, E:H.243 ADP.55: 18 residues within 4Å: Chain E: P.690, V.713, R.715, 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.46, K.47 12 PLIP interactions: 12 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:V.787, E:S.789, E:S.789, E:E.841 Salt bridges: E:R.715, E:H.788 ADP.74: 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.61, MN.62, PO4.73 19 PLIP interactions: 19 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, G:N.301 Water bridges: G:T.173, G:T.173, G:H.243, G:T.244 Salt bridges: G:R.129, G:R.129, G:R.169, G:H.243 ADP.75: 17 residues within 4Å: Chain G: P.690, R.715, 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.66, K.67 13 PLIP interactions: 13 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, G:E.841 Water bridges: G:H.788 Salt bridges: G:R.715, G:H.788

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

ORN.16: 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.895, A:L.907 Hydrogen bonds: A:D.791, A:A.793, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:H.1039, A:Y.1040, A:T.1043 ORN.19: 7 residues within 4Å: Chain A: R.528, A.537, T.538, E.552, N.554 Chain B: R.120, R.123 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.538, A:T.538, A:E.552, A:N.554 Water bridges: B:R.123, B:R.123 Salt bridges: B:R.120, B:R.123 ORN.36: 9 residues within 4Å: Chain C: E.783, D.791, A.793, E.892, V.893, L.907, Y.1040, D.1041, T.1042 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.791, C:A.793, C:D.1041, C:T.1042, C:T.1043 ORN.39: 8 residues within 4Å: Chain C: R.528, A.537, T.538, D.539, E.552, N.554 Chain D: R.120, R.123 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Water bridges: D:R.120, D:R.123, D:R.123 Salt bridges: D:R.120, D:R.123 Hydrogen bonds: C:T.538, C:T.538, C:D.539, C:E.552 ORN.56: 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 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.895, E:L.907 Hydrogen bonds: E:E.783, E:A.793, E:D.1041, E:D.1041, E:T.1042, E:T.1043 Water bridges: E:L.907 ORN.59: 7 residues within 4Å: Chain E: R.528, A.537, T.538, E.552, N.554 Chain F: R.120, R.123 12 PLIP interactions: 6 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:T.538, E:T.538, E:E.552, E:N.554, F:R.120 Water bridges: E:R.343, E:D.539, F:R.123, F:R.123, F:R.123 Salt bridges: F:R.120, F:R.123 ORN.76: 11 residues within 4Å: Chain G: E.783, D.791, S.792, 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:D.791, G:A.793, G:D.1041, G:T.1042 Water bridges: G:Y.1040 ORN.79: 7 residues within 4Å: Chain G: R.528, A.537, T.538, E.552, N.554 Chain H: R.120, R.123 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain G Water bridges: H:R.123 Salt bridges: H:R.120, H:R.123 Hydrogen bonds: G:R.528, G:T.538, G:T.538, G:N.554

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.17: 19 residues within 4Å: Chain A: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993, V.994, H.995, I.1001, N.1015, T.1016, T.1017, D.1025, S.1026, V.1028, I.1029, R.1030 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.974, A:G.976, A:T.977, A:T.977, A:V.994, A:N.1015, A:N.1015, A:T.1017, A:S.1026, A:R.1030 Water bridges: A:H.995, A:H.995 Salt bridges: A:K.954, A:K.993 IMP.37: 18 residues within 4Å: Chain C: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993, V.994, H.995, I.1001, N.1015, T.1016, T.1017, D.1025, S.1026, V.1028, R.1030 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.948, C:T.974, C:G.976, C:T.977, C:V.994, C:H.995, C:N.1015, C:N.1015, C:S.1026, C:R.1030 Water bridges: C:H.995, C:H.995, C:S.1018 Salt bridges: C:K.954, C:K.993 IMP.57: 17 residues within 4Å: Chain E: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993, V.994, I.1001, N.1015, T.1016, T.1017, D.1025, S.1026, V.1028, R.1030 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:T.974, E:G.976, E:T.977, E:T.977, E:K.993, E:V.994, E:N.1015, E:N.1015, E:S.1026, E:R.1030 Water bridges: E:K.954, E:K.954, E:H.995, E:H.995 Salt bridges: E:K.954, E:K.993 IMP.77: 17 residues within 4Å: Chain G: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993, V.994, H.995, I.1001, N.1015, T.1016, T.1017, D.1025, S.1026, R.1030 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:T.974, G:G.976, G:T.977, G:K.993, G:V.994, G:N.1015, G:N.1015, G:S.1026, G:R.1030 Water bridges: G:S.1018, G:D.1025 Salt bridges: G:K.954, G:K.993

4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.18: 6 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.10 No protein-ligand interaction detected (PLIP) NET.38: 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.58: 6 residues within 4Å: Chain E: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.50 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.93 NET.78: 5 residues within 4Å: Chain G: Q.22, Q.93, T.94, N.97 Ligands: CL.70 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Q.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase. J.Biol.Chem. (1999)

Release Date

1999-07-26

Peptides

PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE): ACEG
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE): 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

PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)

PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)

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