SMTL ID : 1bxr.1 (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-4-4-mer

Ligands

13 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.299, N.301 Ligands: K.3, ANP.10 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.11 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.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.841, A:E.841, H2O.9 MN.16: 4 residues within 4Å: Chain C: E.299, N.301 Ligands: K.18, ANP.27 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.45 MN.19: 4 residues within 4Å: Chain C: Q.829, E.841 Ligands: MN.20, ANP.28 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.841, H2O.50 MN.20: 5 residues within 4Å: Chain C: V.719, E.841, N.843 Ligands: MN.19, ANP.28 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.841, C:E.841, H2O.42 MN.26: 2 residues within 4Å: Chain C: H.150, E.154 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.150, C:E.154, C:E.154, H2O.46 MN.33: 4 residues within 4Å: Chain E: E.299, N.301 Ligands: K.35, ANP.43 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.78 MN.36: 4 residues within 4Å: Chain E: Q.829, E.841 Ligands: MN.37, ANP.44 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.841 MN.37: 6 residues within 4Å: Chain E: R.675, V.719, E.841, N.843 Ligands: MN.36, ANP.44 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.841, E:E.841, H2O.75 MN.47: 5 residues within 4Å: Chain G: R.129, E.299, N.301 Ligands: K.49, ANP.58 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.110 MN.50: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ANP.59 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.841, H2O.115 MN.51: 4 residues within 4Å: Chain G: V.719, E.841, N.843 Ligands: ANP.59 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.841, G:E.841, H2O.107

19 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 Ligand excluded by PLIP K.3: 6 residues within 4Å: Chain A: A.126, E.127, E.299, M.300, N.301 Ligands: MN.1 Ligand excluded by PLIP K.6: 6 residues within 4Å: Chain A: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.15: 2 residues within 4Å: Chain B: H.16, D.112 Ligand excluded by PLIP K.17: 6 residues within 4Å: Chain C: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.18: 6 residues within 4Å: Chain C: A.126, E.127, E.299, M.300, N.301 Ligands: MN.16 Ligand excluded by PLIP K.21: 6 residues within 4Å: Chain C: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.25: 3 residues within 4Å: Chain C: T.143, A.144, R.145 Ligand excluded by PLIP K.32: 2 residues within 4Å: Chain D: H.16, D.112 Ligand excluded by PLIP K.34: 6 residues within 4Å: Chain E: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.35: 6 residues within 4Å: Chain E: A.126, E.127, E.299, M.300, N.301 Ligands: MN.33 Ligand excluded by PLIP K.38: 6 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.41: 1 residues within 4Å: Chain E: K.35 Ligand excluded by PLIP K.42: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.48: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.49: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.47 Ligand excluded by PLIP K.52: 6 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.57: 2 residues within 4Å: Chain G: C.551, N.554 Ligand excluded by PLIP K.62: 2 residues within 4Å: Chain H: H.16, D.112 Ligand excluded by PLIP

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

CL.7: 5 residues within 4Å: Chain A: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.475, N.485, F.488 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: N.289, N.292, R.294 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: E.549 Chain B: F.15, I.113, D.114 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: Q.93, T.173, M.174 Ligands: NET.30 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain C: E.549 Chain D: F.15, H.16, I.113, D.114 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain E: A.15, G.16, I.18, A.23, F.26 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain E: S.854, H.1069 Ligand excluded by PLIP CL.53: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain G: K.475, N.485 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain G: K.940, K.941, H.942 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain G: N.289, N.292, R.294 Ligand excluded by PLIP

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

ANP.10: 26 residues within 4Å: Chain A: R.129, A.144, I.167, R.169, T.173, M.174, G.175, G.176, D.207, E.208, 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 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.129, A:R.129, A:G.175, A:G.176, A:E.208, A:L.210, A:E.215, A:G.241, A:I.242, A:H.243, A:T.244, A:Q.285, A:E.299, A:N.301, A:R.303, A:R.306, A:R.306 Water bridges: A:N.301, A:R.303 Salt bridges: A:R.129, A:R.169 ANP.11: 28 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, I.840, E.841, N.843, R.845, R.848, P.909 Ligands: MN.4, MN.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.675, A:R.675, A:R.715, A:G.721, A:G.722, A:D.753, A:D.753, A:L.756, A:E.761, A:G.786, A:S.789, A:S.789, A:Q.829, A:N.843, A:R.845, A:R.848, A:R.848 Water bridges: A:S.789, A:Q.829 Salt bridges: A:R.675, A:R.715 ANP.27: 26 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, N.301, R.303, R.306, T.376 Ligands: MN.16 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:R.129, C:T.173, C:G.175, C:G.176, C:E.208, C:L.210, C:E.215, C:G.241, C:H.243, C:T.244, C:Q.285, C:E.299, C:N.301, C:R.303, C:R.306, C:R.306 Water bridges: C:T.173, C:R.303 Salt bridges: C:R.129, C:R.169 ANP.28: 27 residues within 4Å: Chain C: 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.19, MN.20 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:R.675, C:R.675, C:R.715, C:V.719, C:G.721, C:G.722, C:R.723, C:D.753, C:L.756, C:E.761, C:G.786, C:H.788, C:S.789, C:Q.829, C:Q.829, C:E.841, C:E.841, C:N.843, C:R.845, C:R.848, C:R.848 Salt bridges: C:R.675, C:R.715 ANP.43: 25 residues within 4Å: Chain E: R.129, I.167, R.169, T.173, M.174, G.175, G.176, D.207, E.208, 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.33 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:R.129, E:R.129, E:G.175, E:G.176, E:E.208, E:L.210, E:E.215, E:G.241, E:I.242, E:H.243, E:T.244, E:Q.285, E:E.299, E:N.301, E:R.303, E:R.306, E:R.306 Water bridges: E:R.303, E:R.303 Salt bridges: E:R.129, E:R.169 ANP.44: 28 residues within 4Å: Chain E: 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, I.840, E.841, N.843, R.845, R.848, P.909 Ligands: MN.36, MN.37 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:R.675, E:R.675, E:R.715, E:G.721, E:G.722, E:R.723, E:D.753, E:D.753, E:L.756, E:E.761, E:G.786, E:S.789, E:N.843, E:R.845, E:R.848, E:R.848 Water bridges: E:R.845 Salt bridges: E:R.675, E:R.715 ANP.58: 26 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, N.301, R.303, R.306, T.376 Ligands: MN.47 23 PLIP interactions: 23 interactions with chain G Hydrogen bonds: G:R.129, G:R.129, G:R.169, G:G.175, G:G.176, G:E.208, G:L.210, G:E.215, G:G.241, G:I.242, G:H.243, G:T.244, G:Q.285, G:E.299, G:N.301, G:R.303, G:R.306, G:R.306 Water bridges: G:R.303, G:R.303 Salt bridges: G:R.129, G:R.169, G:H.243 ANP.59: 27 residues within 4Å: Chain G: R.675, P.690, 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, I.840, E.841, N.843, R.845, R.848, P.909 Ligands: MN.50, MN.51 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:R.675, G:R.675, G:R.715, G:G.721, G:G.722, G:D.753, G:L.756, G:E.761, G:G.786, G:S.789, G:Q.829, G:N.843, G:R.845, G:R.848, G:R.848 Salt bridges: G:R.675, G:R.715

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

ORN.12: 10 residues within 4Å: Chain A: E.783, D.791, S.792, A.793, E.892, V.893, L.907, Y.1040, D.1041, T.1042 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.892, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:T.1043 ORN.29: 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 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.895 Hydrogen bonds: C:D.791, C:D.1041, C:T.1042 Water bridges: C:E.783, C:Y.1040 ORN.45: 9 residues within 4Å: Chain E: E.783, D.791, A.793, E.892, V.893, L.907, Y.1040, D.1041, T.1042 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.791, E:A.793, E:D.1041, E:D.1041, E:T.1042 Water bridges: E:Y.1040, E:Y.1040, E:T.1043 ORN.60: 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 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.895 Hydrogen bonds: G:E.783, G:D.1041, G:T.1042 Water bridges: G:Y.1040, G:T.1043

4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.13: 5 residues within 4Å: Chain A: Q.22, Q.93, T.94, N.97, N.936 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.22, A:Q.93 NET.30: 6 residues within 4Å: Chain C: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.22 No protein-ligand interaction detected (PLIP) NET.46: 5 residues within 4Å: Chain E: Q.22, Q.93, T.94, N.97, N.936 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.93 NET.61: 5 residues within 4Å: Chain G: Q.22, Q.93, T.94, N.97, N.936 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: ACEG
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

CARBAMOYL-PHOSPHATE SYNTHASE

CARBAMOYL-PHOSPHATE SYNTHASE

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