SMTL ID : 5tkv.1

X-RAY CRYSTAL STRUCTURE OF THE "CLOSED" CONFORMATION OF CTP-INHIBITED E. COLI CYTIDINE TRIPHOSPHATE (CTP) SYNTHETASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x GLN: GLUTAMINE(Non-covalent)

GLN.1: 12 residues within 4Å: Chain A: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.488, H.489, R.490, Y.491, H.535 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.373 Hydrogen bonds: A:G.372, A:L.400, A:Q.403, A:E.423, A:R.490, A:Y.491, A:Y.491, A:H.535 GLN.11: 12 residues within 4Å: Chain B: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.488, H.489, R.490, Y.491, H.535 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.373 Hydrogen bonds: B:L.400, B:Q.403, B:E.423, B:R.488, B:R.490, B:Y.491, Q.11, Q.11 GLN.19: 12 residues within 4Å: Chain C: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.488, H.489, R.490, Y.491, H.535 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:F.373 Hydrogen bonds: C:G.372, C:L.400, C:Q.403, C:E.423, C:R.490, C:Y.491, C:Y.491, C:H.535 GLN.29: 12 residues within 4Å: Chain D: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.488, H.489, R.490, Y.491, H.535 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.373 Hydrogen bonds: D:L.400, D:Q.403, D:E.423, D:R.488, D:R.490, D:Y.491, Q.29, Q.29

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

SO4.2: 7 residues within 4Å: Chain A: S.35, L.36, G.37, K.38, G.39, E.160 Ligands: SO4.3 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: K.38, K.60, E.160, G.162, G.163 Ligands: SO4.2 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.386, R.411, H.412 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: K.317, F.373, R.376 Ligand excluded by PLIP SO4.12: 7 residues within 4Å: Chain B: S.35, L.36, G.37, K.38, G.39, E.160 Ligands: SO4.13 Ligand excluded by PLIP SO4.13: 7 residues within 4Å: Chain B: K.38, K.60, D.62, E.160, G.162, G.163 Ligands: SO4.12 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: R.411, H.412 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: K.317, R.376 Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain C: S.35, L.36, G.37, K.38, G.39, E.160 Ligands: SO4.21 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain C: K.38, K.60, E.160, G.162, G.163 Ligands: SO4.20 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: R.386, R.411, H.412 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: K.317, F.373, R.376 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain D: S.35, L.36, G.37, K.38, G.39, E.160 Ligands: SO4.31 Ligand excluded by PLIP SO4.31: 7 residues within 4Å: Chain D: K.38, K.60, D.62, E.160, G.162, G.163 Ligands: SO4.30 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: R.411, H.412 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain D: K.317, R.376 Ligand excluded by PLIP

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

MPD.4: 7 residues within 4Å: Chain A: R.231, K.259, D.260, V.261, I.264, I.267 Chain B: A.202 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.202, A:I.264 Hydrogen bonds: A:V.261 MPD.14: 7 residues within 4Å: Chain B: R.231, L.258, K.259, D.260, V.261, I.264, I.267 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.258, B:I.264, B:I.267 Hydrogen bonds: B:R.231, B:V.261 MPD.22: 7 residues within 4Å: Chain C: R.231, K.259, D.260, V.261, I.264, I.267 Chain D: A.202 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.202, C:I.264 Hydrogen bonds: C:V.261 MPD.32: 7 residues within 4Å: Chain D: R.231, L.258, K.259, D.260, V.261, I.264, I.267 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.258, D:I.264, D:I.267 Hydrogen bonds: D:R.231, D:V.261

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 1 residues within 4Å: Ligands: CTP.10 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: CTP.8 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Ligands: CTP.28 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Ligands: CTP.26 No protein-ligand interaction detected (PLIP)

4 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.8: 14 residues within 4Å: Chain A: S.34, D.167, I.168, E.169 Chain B: K.207, T.208, K.209, Q.212, K.243, F.247 Chain C: Q.134, V.135, I.136 Ligands: MG.9 36 PLIP interactions: 10 interactions with chain A, 22 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:S.34, A:S.34, A:D.167, A:I.168, A:E.169, B:T.208, B:T.208, B:T.208, B:K.209, B:K.209, B:Q.212, C:V.135, C:I.136 Water bridges: A:S.34, A:G.166, A:D.167, A:E.169, A:E.169, B:K.207, B:K.216, B:K.216, B:K.243, B:K.243, B:K.243, B:K.243, B:K.243, C:E.175 Hydrophobic interactions: B:F.247, C:I.136 Salt bridges: B:K.207, B:K.207, B:K.209, B:K.209, B:K.209, B:K.243, B:K.243 CTP.10: 14 residues within 4Å: Chain A: K.207, T.208, K.209, Q.212, K.243, F.247 Chain B: S.34, D.167, I.168, E.169 Chain D: Q.134, V.135, I.136 Ligands: MG.7 29 PLIP interactions: 7 interactions with chain B, 18 interactions with chain A, 4 interactions with chain D Hydrogen bonds: B:S.34, B:S.34, B:I.168, B:E.169, A:T.208, A:K.209, A:K.209, A:Q.212, D:V.135, D:I.136 Water bridges: B:S.34, B:E.169, B:E.169, A:K.207, A:K.207, A:K.216, A:K.216, A:K.243, A:K.243, D:E.175 Hydrophobic interactions: A:F.247, D:I.136 Salt bridges: A:K.207, A:K.207, A:K.209, A:K.209, A:K.209, A:K.243, A:K.243 CTP.26: 14 residues within 4Å: Chain A: Q.134, V.135, I.136 Chain C: S.34, D.167, I.168, E.169 Chain D: K.207, T.208, K.209, Q.212, K.243, F.247 Ligands: MG.27 36 PLIP interactions: 10 interactions with chain C, 22 interactions with chain D, 4 interactions with chain A Hydrogen bonds: C:S.34, C:S.34, C:D.167, C:I.168, C:E.169, D:T.208, D:T.208, D:T.208, D:K.209, D:K.209, D:Q.212, A:V.135, A:I.136 Water bridges: C:S.34, C:G.166, C:D.167, C:E.169, C:E.169, D:K.207, D:K.216, D:K.216, D:K.243, D:K.243, D:K.243, D:K.243, D:K.243, A:E.175 Hydrophobic interactions: D:F.247, A:I.136 Salt bridges: D:K.207, D:K.207, D:K.209, D:K.209, D:K.209, D:K.243, D:K.243 CTP.28: 14 residues within 4Å: Chain B: Q.134, V.135, I.136 Chain C: K.207, T.208, K.209, Q.212, K.243, F.247 Chain D: S.34, D.167, I.168, E.169 Ligands: MG.25 29 PLIP interactions: 18 interactions with chain C, 4 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: C:F.247, B:I.136 Hydrogen bonds: C:T.208, C:K.209, C:K.209, C:Q.212, B:V.135, B:I.136, D:S.34, D:S.34, D:I.168, D:E.169 Water bridges: C:K.207, C:K.207, C:K.216, C:K.216, C:K.243, C:K.243, B:E.175, D:S.34, D:E.169, D:E.169 Salt bridges: C:K.207, C:K.207, C:K.209, C:K.209, C:K.209, C:K.243, C:K.243

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.17: 2 residues within 4Å: Chain B: I.329, K.333 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.329, B:K.333 MRD.18: 3 residues within 4Å: Chain B: E.303, P.306, S.342 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.342 MRD.35: 2 residues within 4Å: Chain D: I.329, K.333 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.329, D:K.333 MRD.36: 3 residues within 4Å: Chain D: E.303, P.306, S.342 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., Human CTP synthase filament structure reveals the active enzyme conformation. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-04-26

Peptides

CTP synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CTP synthase