SMTL ID : 1bxr.3 (4 other biounits)

STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE COMPLEXED WITH THE ATP ANALOG AMPPNP

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: 4 residues within 4Å: Chain A: E.299, N.301 Ligands: K.3, ANP.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.12 MN.4: 4 residues within 4Å: Chain A: Q.829, E.841 Ligands: MN.5, ANP.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, H2O.17 MN.5: 5 residues within 4Å: Chain A: V.719, E.841, N.843 Ligands: MN.4, ANP.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, A:E.841, H2O.9 MN.11: 2 residues within 4Å: Chain A: H.150, E.154 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.150, A:E.154, A:E.154, H2O.13

5 x K: POTASSIUM ION(Non-covalent)

K.2: 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.3: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:E.299, A:M.300, H2O.5, H2O.5 K.6: 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.10: 3 residues within 4Å: Chain A: T.143, A.144, R.145 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.143, A:T.143, A:A.144, H2O.2 K.17: 2 residues within 4Å: Chain B: H.16, D.112 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.16, B:D.112, H2O.8, H2O.27

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

CL.7: 4 residues within 4Å: Chain A: Q.93, T.173, M.174 Ligands: NET.15 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: E.549 Chain B: F.15, H.16, I.113, D.114 Ligand excluded by PLIP

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.12: 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, R.303, R.306, T.376 Ligands: MN.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.129, A:G.175, A:G.176, A:E.208, A:L.210, A:E.215, A:G.241, A:H.243, A:T.244, A:Q.285, A:E.299, A:R.303, A:R.306, A:R.306 Water bridges: A:T.173, A:N.301, A:R.303 Salt bridges: A:R.129, A:R.169 ANP.13: 27 residues within 4Å: Chain A: R.675, P.690, V.713, R.715, V.719, L.720, G.721, G.722, M.725, D.753, H.754, F.755, L.756, E.761, A.785, G.786, V.787, H.788, S.789, Q.829, E.841, N.843, R.845, R.848, P.909 Ligands: MN.4, MN.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.675, A:R.675, A:R.715, A:G.721, A:G.722, A:R.723, A:D.753, A:L.756, A:E.761, A:G.786, A:S.789, A:Q.829, A:R.845, A:R.848, A:R.848 Salt bridges: A:R.675, A:R.715

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

ORN.14: 10 residues within 4Å: Chain A: E.783, D.791, A.793, E.892, V.893, L.895, L.907, Y.1040, D.1041, T.1042 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.895 Hydrogen bonds: A:D.791, A:D.1041, A:T.1042 Water bridges: A:E.783, A:Y.1040

1 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.15: 6 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. Biochemistry (1999)

Release Date

1999-04-20

Peptides

CARBAMOYL-PHOSPHATE SYNTHASE: A
CARBAMOYL-PHOSPHATE SYNTHASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

CARBAMOYL-PHOSPHATE SYNTHASE

CARBAMOYL-PHOSPHATE SYNTHASE

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