SMTL ID : 1t36.1

Crystal structure of E. coli carbamoyl phosphate synthetase small subunit mutant C248D complexed with uridine 5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-oligomer

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, PO4.5, ADP.67 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, A:E.299, H2O.100 MN.2: 6 residues within 4Å: Chain A: H.243, Q.285, E.299 Ligands: MN.1, PO4.5, ADP.67 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.514 MN.6: 3 residues within 4Å: Chain A: Q.829, E.841 Ligands: ADP.68 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.841, H2O.517, H2O.812 MN.15: 7 residues within 4Å: Chain C: M.174, E.299, N.301 Ligands: MN.16, K.18, PO4.19, ADP.72 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, C:E.299, H2O.1110 MN.16: 6 residues within 4Å: Chain C: H.243, Q.285, E.299 Ligands: MN.15, PO4.19, ADP.72 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.299, H2O.1506 MN.20: 3 residues within 4Å: Chain C: Q.829, E.841 Ligands: ADP.73 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.841, H2O.1508, H2O.1509 MN.32: 7 residues within 4Å: Chain E: M.174, E.299, N.301 Ligands: MN.33, K.35, PO4.36, ADP.77 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, E:E.299, H2O.2152 MN.33: 6 residues within 4Å: Chain E: H.243, Q.285, E.299 Ligands: MN.32, PO4.36, ADP.77 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.299, H2O.2556 MN.37: 3 residues within 4Å: Chain E: Q.829, E.841 Ligands: ADP.78 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.841, H2O.2560, H2O.2561 MN.49: 7 residues within 4Å: Chain G: M.174, E.299, N.301 Ligands: MN.50, K.52, PO4.53, ADP.82 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, G:E.299, H2O.3181 MN.50: 6 residues within 4Å: Chain G: H.243, Q.285, E.299 Ligands: MN.49, PO4.53, ADP.82 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.299, H2O.3540 MN.54: 3 residues within 4Å: Chain G: Q.829, E.841 Ligands: ADP.83 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.841, H2O.3541, H2O.3542

22 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.7: 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: T.143, A.144, R.145 Ligand excluded by PLIP K.14: 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.15 Ligand excluded by PLIP K.21: 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.23: 3 residues within 4Å: Chain C: T.143, A.144, R.145 Ligand excluded by PLIP K.28: 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.32 Ligand excluded by PLIP K.38: 7 residues within 4Å: Chain E: E.761, H.781, E.783, Q.784, A.785, V.787, S.792 Ligand excluded by PLIP K.39: 3 residues within 4Å: Chain E: D.84, G.112, T.114 Ligand excluded by PLIP K.41: 2 residues within 4Å: Chain E: T.143, A.144 Ligand excluded by PLIP K.46: 2 residues within 4Å: Chain F: H.16, D.112 Ligand excluded by PLIP K.51: 6 residues within 4Å: Chain G: E.215, N.236, D.238, A.239, I.242, S.247 Ligand excluded by PLIP K.52: 6 residues within 4Å: Chain G: A.126, E.127, E.299, M.300, N.301 Ligands: MN.49 Ligand excluded by PLIP K.55: 6 residues within 4Å: Chain G: E.761, H.781, E.783, Q.784, V.787, S.792 Ligand excluded by PLIP K.56: 3 residues within 4Å: Chain G: D.84, G.112, T.114 Ligand excluded by PLIP K.58: 3 residues within 4Å: Chain G: T.143, A.144, R.145 Ligand excluded by PLIP K.63: 2 residues within 4Å: Chain H: H.16, D.112 Ligand excluded by PLIP

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

PO4.5: 11 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, ADP.67 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.175, A:N.301 Water bridges: A:Q.285, A:R.303, A:S.305, A:R.306 Salt bridges: A:H.243, A:R.303, A:R.306 PO4.19: 11 residues within 4Å: Chain C: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.15, MN.16, ADP.72 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.175 Water bridges: C:T.244, C:T.244, C:R.303, C:R.303, C:S.305, C:R.306 Salt bridges: C:H.243, C:R.303, C:R.306 PO4.31: 2 residues within 4Å: Chain C: E.560, D.592 No protein-ligand interaction detected (PLIP) PO4.36: 11 residues within 4Å: Chain E: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.32, MN.33, ADP.77 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 PO4.53: 11 residues within 4Å: Chain G: M.174, G.175, H.243, Q.285, E.299, N.301, R.303, R.306 Ligands: MN.49, MN.50, ADP.82 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.175, G:N.301 Water bridges: G:T.244, G:T.244, G:Q.285, G:R.303, G:S.305, G:R.306 Salt bridges: G:H.243, G:R.303, G:R.306

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

CL.8: 5 residues within 4Å: Chain A: Q.93, T.173, M.174, S.177 Ligands: NET.70 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: H.70, W.71 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.13: 3 residues within 4Å: Chain A: K.475, N.485, F.488 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain C: Q.93, T.173, M.174, S.177 Ligands: NET.75 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: H.70, W.71 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain C: N.289, N.292, R.294 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: K.475, N.485 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: E.549 Chain D: F.15, H.16, I.113, D.114 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain E: Q.93, T.173, M.174, S.177 Ligands: NET.80 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain E: W.71 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain E: W.213, N.289, N.292, R.294 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain E: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain E: K.475, N.485, F.488 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain E: E.549 Chain F: F.15, I.113, D.114 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain E: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain G: Q.93, T.173, M.174 Ligands: NET.85 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain G: H.70, W.71 Ligand excluded by PLIP CL.60: 3 residues within 4Å: Chain G: N.289, N.292, R.294 Ligand excluded by PLIP CL.61: 5 residues within 4Å: Chain G: A.370, N.371, F.900, P.901, G.902 Ligand excluded by PLIP CL.62: 3 residues within 4Å: Chain G: K.475, N.485, F.488 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain G: E.549 Chain H: F.15, I.113, D.114 Ligand excluded by PLIP CL.65: 4 residues within 4Å: Chain G: F.578, R.845, A.847, R.848 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain H: S.169, W.170, T.171, Q.172, A.184 Ligand excluded by PLIP

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

ADP.67: 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, PO4.5 18 PLIP interactions: 18 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:E.299, A:N.301 Water bridges: A:R.129, A:R.129, A:Q.285 Salt bridges: A:R.129, A:R.129, A:R.169, A:H.243 ADP.68: 17 residues within 4Å: Chain A: 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.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:H.754, A:L.756, A:E.761, A:G.786, A:S.789, A:S.789, A:E.841 Water bridges: A:R.715, A:R.715, A:Q.829, A:Q.829, A:E.841, A:E.841, A:E.841 Salt bridges: A:R.715, A:H.788 ADP.72: 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.15, MN.16, PO4.19 18 PLIP interactions: 18 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, C:E.299 Water bridges: C:T.173, C:T.173, C:H.243, C:Q.285 Salt bridges: C:R.129, C:R.129, C:R.169, C:H.243 ADP.73: 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, P.909 Ligands: MN.20 18 PLIP interactions: 18 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:Q.829, C:E.841 Water bridges: C:Q.829, C:Q.829, C:Q.829, C:E.841, C:E.841, C:N.843, C:R.848 Salt bridges: C:R.715, C:H.788 ADP.77: 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.32, MN.33, PO4.36 19 PLIP interactions: 19 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:I.242, E:T.244, E:Q.285, E:E.299, E:E.299 Water bridges: E:R.129, E:R.129, E:Q.285 Salt bridges: E:R.129, E:R.129, E:R.169, E:H.243 ADP.78: 18 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.37 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:H.754, E:L.756, E:E.761, E:G.786, E:S.789, E:S.789, E:E.841 Water bridges: E:R.715, E:H.788, E:S.789, E:Q.829, E:Q.829, E:Q.829, E:E.841, E:E.841 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.49, MN.50, PO4.53 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:T.173, 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, G:E.299 Water bridges: G:R.129, G:T.173, G:H.243, G:T.244 Salt bridges: G:R.129, G:R.129, G:R.169, G:H.243 ADP.83: 16 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.54 17 PLIP interactions: 17 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:S.789, G:E.841 Water bridges: G:D.753, G:H.788, G:Q.829, G:Q.829, G:E.841, G:N.843, G:N.843 Salt bridges: G:R.715, G:H.788

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

ORN.69: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.907 Hydrogen bonds: A:D.791, A:A.793, A:D.1041, A:D.1041, A:T.1042 Water bridges: A:T.1043 ORN.74: 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 Water bridges: C:E.783, C:Y.1040 ORN.79: 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 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.895 Hydrogen bonds: E:D.791, E:A.793, E:D.1041, E:D.1041, E:T.1042 Water bridges: E:Y.1040, 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 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.895 Hydrogen bonds: G:D.791, G:A.793, G:D.1041, G:T.1042 Water bridges: G:T.1043

4 x NET: TETRAETHYLAMMONIUM ION(Non-covalent)

NET.70: 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.75: 6 residues within 4Å: Chain C: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.93 NET.80: 6 residues within 4Å: Chain E: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.40 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.93 NET.85: 6 residues within 4Å: Chain G: Q.22, Q.93, T.94, N.97, N.936 Ligands: CL.57 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Q.93

4 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.71: 17 residues within 4Å: Chain A: S.948, V.949, R.950, K.954, T.974, H.975, G.976, T.977, K.993, H.995, N.1015, T.1016, T.1017, A.1022, D.1025, S.1026, I.1029 30 PLIP interactions: 15 interactions with chain A, 15 interactions with chain C Hydrophobic interactions: A:K.993, A:I.1029, C:K.993, C:I.1029 Hydrogen bonds: A:T.974, A:T.974, A:G.976, A:T.977, A:T.977, A:N.1015, A:T.1016, A:S.1026, C:T.974, C:T.974, C:G.976, C:T.977, C:N.1015, C:N.1015, C:S.1026 Water bridges: A:V.994, A:S.1018, C:V.994, C:H.995, C:S.1018 Salt bridges: A:K.954, A:K.993, C:K.954, C:K.993 pi-Cation interactions: A:K.993, C:K.993 U.76: 16 residues within 4Å: Chain C: S.948, V.949, K.954, T.974, H.975, G.976, T.977, K.993, H.995, N.1015, T.1016, T.1017, A.1022, D.1025, S.1026, I.1029 Protein-ligand interaction information (PLIP) not available U.81: 17 residues within 4Å: Chain E: S.948, V.949, R.950, K.954, T.974, H.975, G.976, T.977, K.993, H.995, N.1015, T.1016, T.1017, A.1022, D.1025, S.1026, I.1029 29 PLIP interactions: 16 interactions with chain E, 13 interactions with chain G Hydrophobic interactions: E:K.993, E:I.1029, G:K.993, G:I.1029 Hydrogen bonds: E:T.974, E:T.974, E:G.976, E:T.977, E:T.977, E:H.995, E:N.1015, E:N.1015, E:S.1026, G:T.974, G:T.974, G:G.976, G:T.977, G:N.1015, G:N.1015, G:S.1026 Water bridges: E:V.994, E:S.1018, G:V.994 Salt bridges: E:K.954, E:K.993, G:K.954, G:K.993 pi-Cation interactions: E:K.993, G:K.993 U.86: 17 residues within 4Å: Chain G: S.948, V.949, R.950, K.954, T.974, H.975, G.976, T.977, K.993, H.995, N.1015, T.1016, T.1017, A.1022, D.1025, S.1026, I.1029 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Long-range allosteric transitions in carbamoyl phosphate synthetase. Protein Sci. (2004)

Release Date

2004-09-21

Peptides

Carbamoyl-phosphate synthase large chain: ACEG
Carbamoyl-phosphate synthase small chain: 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 large chain

Carbamoyl-phosphate synthase small chain

Related Entries With Identical Sequence