SMTL ID : 1s1m.1

Crystal Structure of E. Coli CTP Synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: S.15, L.16, G.17, K.18, G.19, D.72 Ligands: SO4.2, MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.16, A:G.17, A:K.18, A:G.19 Water bridges: A:S.15, A:H.75 Salt bridges: A:K.18 SO4.2: 8 residues within 4Å: Chain A: K.18, K.40, E.140, G.142, G.143 Ligands: SO4.1, MG.3, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.143 Water bridges: A:K.40 Salt bridges: A:K.18, A:K.40 SO4.15: 8 residues within 4Å: Chain B: S.15, L.16, G.17, K.18, G.19, D.72 Ligands: SO4.16, MG.17 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.15, B:L.16, B:G.17, B:K.18, B:G.19 Water bridges: B:I.20 Salt bridges: B:K.18 SO4.16: 8 residues within 4Å: Chain B: K.18, K.40, D.72, G.142, G.143 Ligands: SO4.15, MG.17, MG.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.140, B:G.143 Salt bridges: B:K.18, B:K.40 SO4.27: 8 residues within 4Å: Chain C: S.15, L.16, G.17, K.18, G.19, D.72 Ligands: SO4.28, MG.29 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.16, C:G.17, C:K.18, C:G.19 Water bridges: C:S.15, C:H.75 Salt bridges: C:K.18 SO4.28: 8 residues within 4Å: Chain C: K.18, K.40, E.140, G.142, G.143 Ligands: SO4.27, MG.29, MG.30 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.143 Water bridges: C:K.40 Salt bridges: C:K.18, C:K.40 SO4.41: 8 residues within 4Å: Chain D: S.15, L.16, G.17, K.18, G.19, D.72 Ligands: SO4.42, MG.43 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.15, D:L.16, D:G.17, D:K.18, D:G.19 Water bridges: D:I.20 Salt bridges: D:K.18 SO4.42: 8 residues within 4Å: Chain D: K.18, K.40, D.72, G.142, G.143 Ligands: SO4.41, MG.43, MG.44 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.140, D:G.143 Salt bridges: D:K.18, D:K.40

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: K.18, G.19, K.40, D.72, E.140 Ligands: SO4.1, SO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.72, A:E.140 MG.4: 5 residues within 4Å: Chain A: K.40, D.42, P.43, G.142 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.42 MG.17: 5 residues within 4Å: Chain B: G.19, D.72, E.140 Ligands: SO4.15, SO4.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.72, B:E.140 MG.18: 4 residues within 4Å: Chain B: K.40, D.42, P.43 Ligands: SO4.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.42 MG.29: 7 residues within 4Å: Chain C: K.18, G.19, K.40, D.72, E.140 Ligands: SO4.27, SO4.28 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.72, C:E.140 MG.30: 5 residues within 4Å: Chain C: K.40, D.42, P.43, G.142 Ligands: SO4.28 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.42 MG.43: 5 residues within 4Å: Chain D: G.19, D.72, E.140 Ligands: SO4.41, SO4.42 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.72, D:E.140 MG.44: 4 residues within 4Å: Chain D: K.40, D.42, P.43 Ligands: SO4.42 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.42

32 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 3 residues within 4Å: Chain A: S.237, K.239, Q.254 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: L.128, M.160, E.163 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: K.233, D.258, Y.259, K.262 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: P.178 Chain B: P.178 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: K.187, T.188, K.189 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: K.239, V.241, D.242 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: E.64, A.443, V.464, R.466 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: H.193 Chain B: P.190, H.193, S.194 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: S.194 Chain B: H.193 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain B: S.237, K.239, Q.254 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: M.160, E.163 Ligand excluded by PLIP IOD.21: 4 residues within 4Å: Chain A: S.14 Chain B: K.187, T.188, K.189 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain B: Y.259 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain B: V.241, D.242 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain B: D.524 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain B: E.64, A.443, R.466, T.519 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain C: S.237, K.239, Q.254 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain C: L.128, M.160, E.163 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain C: K.233, D.258, Y.259, K.262 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain C: P.178 Chain D: P.178 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain C: K.187, T.188, K.189 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain C: K.239, V.241, D.242 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain C: E.64, A.443, V.464, R.466 Ligand excluded by PLIP IOD.38: 4 residues within 4Å: Chain C: H.193 Chain D: P.190, H.193, S.194 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain C: S.194 Chain D: H.193 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain D: S.237, K.239, Q.254 Ligand excluded by PLIP IOD.46: 2 residues within 4Å: Chain D: M.160, E.163 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain C: S.14 Chain D: K.187, T.188, K.189 Ligand excluded by PLIP IOD.48: 1 residues within 4Å: Chain D: Y.259 Ligand excluded by PLIP IOD.49: 2 residues within 4Å: Chain D: V.241, D.242 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain D: D.524 Ligand excluded by PLIP IOD.51: 4 residues within 4Å: Chain D: E.64, A.443, R.466, T.519 Ligand excluded by PLIP

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.14: 7 residues within 4Å: Chain A: R.211, L.238, K.239, D.240, V.241, I.244 Chain B: A.182 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.182, A:L.238, A:I.244 Hydrogen bonds: A:D.240, A:V.241 MPD.26: 6 residues within 4Å: Chain B: R.211, L.238, K.239, V.241, I.244, I.247 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.238, B:I.244 Hydrogen bonds: B:V.241, B:V.241 MPD.40: 7 residues within 4Å: Chain C: R.211, L.238, K.239, D.240, V.241, I.244 Chain D: A.182 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.238, C:I.244, D:A.182 Hydrogen bonds: C:D.240, C:V.241 MPD.52: 6 residues within 4Å: Chain D: R.211, L.238, K.239, V.241, I.244, I.247 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.238, D:I.244 Hydrogen bonds: D:V.241, D:V.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Endrizzi, J.A. et al., Crystal Structure of Escherichia coli Cytidine Triphosphate Synthetase, a Nucleotide-Regulated Glutamine Amidotransferase/ATP-Dependent Amidoligase Fusion Protein and Homologue of Anticancer and Antiparasitic Drug Targets. Biochemistry (2004)

Release Date

2004-06-15

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CTP synthase

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