SMTL ID : 7mh1.1

Human CTPS2 bound to CTP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

CTP.1: 17 residues within 4Å: Chain A: S.12, G.13, I.14, G.15, K.16, G.17, I.18, S.21, L.69, D.70, N.73, R.76, F.77, T.250, D.312, K.319 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.18, A:N.73 Hydrogen bonds: A:G.15, A:K.16, A:G.17, A:G.17, A:I.18, A:T.250, A:D.312 Salt bridges: A:K.16 CTP.3: 19 residues within 4Å: Chain A: I.11, S.12, D.153, I.154, E.155, G.156 Chain B: Q.192, K.193, T.194, K.195, Q.198, R.202, K.229, F.233 Chain C: Q.112, V.113, V.114, E.161 Ligands: MG.5 22 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:F.233 Hydrogen bonds: B:T.194, B:T.194, B:K.195, B:K.195, B:Q.198, A:S.12, A:D.153, A:I.154, A:E.155, A:E.155, A:E.155, C:V.113, C:V.114 Salt bridges: B:K.193, B:K.193, B:K.195, B:K.195, B:K.229, B:K.229, B:K.229 pi-Cation interactions: B:K.195 CTP.6: 17 residues within 4Å: Chain B: S.12, G.13, I.14, G.15, K.16, G.17, I.18, S.21, L.69, D.70, N.73, R.76, F.77, T.250, D.312, K.319 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.18, B:N.73 Hydrogen bonds: B:S.12, B:G.15, B:K.16, B:G.17, B:G.17, B:I.18, B:T.250, B:D.312 Salt bridges: B:K.16 CTP.8: 19 residues within 4Å: Chain A: Q.192, K.193, T.194, K.195, Q.198, R.202, K.229, F.233 Chain B: I.11, S.12, D.153, I.154, E.155, G.156 Chain D: Q.112, V.113, V.114, E.161 Ligands: MG.4 22 PLIP interactions: 2 interactions with chain D, 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: D:V.113, D:V.114, A:T.194, A:T.194, A:T.194, A:K.195, A:K.195, A:Q.198, B:S.12, B:I.154, B:E.155, B:E.155, B:E.155 Hydrophobic interactions: A:F.233 Salt bridges: A:K.193, A:K.193, A:K.195, A:K.195, A:K.229, A:K.229, A:K.229 pi-Cation interactions: A:K.195 CTP.9: 17 residues within 4Å: Chain C: S.12, G.13, I.14, G.15, K.16, G.17, I.18, S.21, L.69, D.70, N.73, R.76, F.77, T.250, D.312, K.319 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.18, C:N.73 Hydrogen bonds: C:S.12, C:G.15, C:K.16, C:G.17, C:G.17, C:I.18, C:T.250, C:D.312 Salt bridges: C:K.16 CTP.11: 19 residues within 4Å: Chain A: Q.112, V.113, V.114, E.161 Chain C: I.11, S.12, D.153, I.154, E.155, G.156 Chain D: Q.192, K.193, T.194, K.195, Q.198, R.202, K.229, F.233 Ligands: MG.13 22 PLIP interactions: 2 interactions with chain A, 15 interactions with chain D, 5 interactions with chain C Hydrogen bonds: A:V.113, A:V.114, D:T.194, D:T.194, D:T.194, D:K.195, D:K.195, D:Q.198, C:S.12, C:I.154, C:E.155, C:E.155, C:E.155 Hydrophobic interactions: D:F.233 Salt bridges: D:K.193, D:K.193, D:K.195, D:K.195, D:K.229, D:K.229, D:K.229 pi-Cation interactions: D:K.195 CTP.14: 17 residues within 4Å: Chain D: S.12, G.13, I.14, G.15, K.16, G.17, I.18, S.21, L.69, D.70, N.73, R.76, F.77, T.250, D.312, K.319 Ligands: MG.15 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.18, D:N.73 Hydrogen bonds: D:G.15, D:K.16, D:G.17, D:G.17, D:I.18, D:T.250, D:D.312 Salt bridges: D:K.16 CTP.16: 19 residues within 4Å: Chain B: Q.112, V.113, V.114, E.161 Chain C: Q.192, K.193, T.194, K.195, Q.198, R.202, K.229, F.233 Chain D: I.11, S.12, D.153, I.154, E.155, G.156 Ligands: MG.12 22 PLIP interactions: 14 interactions with chain C, 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: C:F.233 Hydrogen bonds: C:T.194, C:T.194, C:K.195, C:K.195, C:Q.198, D:S.12, D:D.153, D:I.154, D:E.155, D:E.155, D:E.155, B:V.113, B:V.114 Salt bridges: C:K.193, C:K.193, C:K.195, C:K.195, C:K.229, C:K.229, C:K.229 pi-Cation interactions: C:K.195

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.17, K.38, D.70 Ligands: CTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.70 MG.4: 4 residues within 4Å: Chain A: E.191, K.193, K.229 Ligands: CTP.8 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: E.191, K.193, K.229 Ligands: CTP.3 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: G.17, K.38, D.70 Ligands: CTP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.70 MG.10: 4 residues within 4Å: Chain C: G.17, K.38, D.70 Ligands: CTP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.70 MG.12: 4 residues within 4Å: Chain C: E.191, K.193, K.229 Ligands: CTP.16 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain D: E.191, K.193, K.229 Ligands: CTP.11 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: G.17, K.38, D.70 Ligands: CTP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., Structural basis for isoform-specific inhibition of human CTPS1. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-10-13

Peptides

CTP synthase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
J

C
K

D
L

CTP synthase 2

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