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

CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

4 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, PO4.6, ADP.23 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.1 MN.2: 7 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, K.5, PO4.6, ADP.23 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.1 MN.7: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: MN.8, ADP.24 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.841, H2O.1, H2O.1 MN.8: 5 residues within 4Å: Chain A: E.841, N.843, R.845 Ligands: MN.7, ADP.24 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, A:E.841, H2O.1

8 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.215, A:D.238, A:A.239, A:I.242, A:S.247 K.4: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.127, A:E.299, A:M.300, H2O.1 K.5: 6 residues within 4Å: Chain A: E.217, T.244, N.283, Q.285 Ligands: MN.2, PO4.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, H2O.1 K.9: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.761, A:H.781, A:Q.784, A:V.787, A:S.792 K.11: 2 residues within 4Å: Chain A: T.143, A.144 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.143, A:T.143, H2O.8, H2O.8 K.12: 5 residues within 4Å: Chain A: A.672, E.673, E.841, V.842, N.843 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.842 K.13: 2 residues within 4Å: Chain A: C.551, N.554 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.551, H2O.19 K.27: 2 residues within 4Å: Chain B: H.16, D.112 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.16, B:D.112, H2O.40

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

PO4.6: 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.23 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:S.305 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.10: 9 residues within 4Å: Chain A: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993 Ligands: GLN.21 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.974, A:T.974, A:T.974, A:G.976, A:T.977, A:T.977 Water bridges: A:K.954, A:K.954, A:K.993 Salt bridges: A:K.954, A:K.993 PO4.20: 3 residues within 4Å: Chain A: E.560, D.592, Y.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.593 Water bridges: A:Y.594

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

CL.14: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.26 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: W.71 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: K.475, N.485, F.488 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: F.15, I.113, D.114 Ligand excluded by PLIP

2 x GLN: GLUTAMINE(Non-covalent)

GLN.21: 11 residues within 4Å: Chain A: S.948, V.949, R.950, K.993, N.1015, T.1016, T.1017, D.1025, S.1026, I.1029 Ligands: PO4.10 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.948, A:S.948, A:N.1015, A:T.1016, Q.21 Water bridges: A:K.993, A:V.994 GLN.22: 8 residues within 4Å: Chain A: R.528, A.537, T.538, D.539, E.552, N.554 Chain B: R.120, R.123 12 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A, 1 Ligand-Ligand interactions Water bridges: B:R.120, B:R.120, B:R.123, B:R.123, A:D.539, Q.22 Salt bridges: B:R.120, B:R.123 Hydrogen bonds: A:T.538, A:D.539, A:E.552, A:N.554

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

ADP.23: 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, PO4.6 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.173, 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:E.299 Water bridges: A:R.129, A:R.129, A:H.243, A:Q.285 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.24: 17 residues within 4Å: Chain A: 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.7, MN.8 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, A:S.789, A:E.841 Water bridges: A:Q.829, A:N.843 Salt bridges: A:R.715, A:H.788

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

ORN.25: 9 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, L.895, L.907, 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:E.783, A:P.905, A:Y.1040

1 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.26: 6 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Acta Crystallogr.,Sect.D (1999)

Release Date

1998-06-17

Peptides

CARBAMOYL PHOSPHATE SYNTHETASE: A
CARBAMOYL PHOSPHATE SYNTHETASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

CARBAMOYL PHOSPHATE SYNTHETASE

CARBAMOYL PHOSPHATE SYNTHETASE

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