SMTL ID : 7mgz.1

Human CTPS1 bound to UTP, AMPPNP, and glutamine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.1: 21 residues within 4Å: Chain A: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.68, G.148, G.149, D.153, E.155 Chain C: K.193, T.194, K.195, Q.198, K.229 Chain D: T.110, Q.112 Ligands: ANP.4, MG.11 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:D.40 Hydrogen bonds: A:K.38, A:D.40, A:P.41, A:H.55, A:G.149, A:D.153, C:T.194, C:K.195, C:Q.198 pi-Stacking: A:H.55 Salt bridges: C:K.193, C:K.193, C:K.195, C:K.195, C:K.229, C:K.229 UTP.6: 21 residues within 4Å: Chain B: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.68, G.148, G.149, D.153, E.155 Chain C: T.110, Q.112 Chain D: K.193, T.194, K.195, Q.198, K.229 Ligands: ANP.9, MG.16 17 PLIP interactions: 9 interactions with chain D, 8 interactions with chain B Hydrogen bonds: D:T.194, D:K.195, D:Q.198, B:K.38, B:D.40, B:P.41, B:H.55, B:G.149, B:D.153 Salt bridges: D:K.193, D:K.193, D:K.195, D:K.195, D:K.229, D:K.229 Hydrophobic interactions: B:D.40 pi-Stacking: B:H.55 UTP.12: 21 residues within 4Å: Chain A: K.193, T.194, K.195, Q.198, K.229 Chain B: T.110, Q.112 Chain C: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.68, G.148, G.149, D.153, E.155 Ligands: MG.5, ANP.15 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:D.40 Hydrogen bonds: C:K.38, C:P.41, C:H.55, C:G.149, C:D.153, C:E.155, A:T.194, A:K.195, A:Q.198 pi-Stacking: C:H.55 Salt bridges: A:K.193, A:K.193, A:K.195, A:K.195, A:K.229, A:K.229 UTP.17: 21 residues within 4Å: Chain A: T.110, Q.112 Chain B: K.193, T.194, K.195, Q.198, K.229 Chain D: S.12, K.16, K.38, D.40, P.41, Y.42, H.55, D.68, G.148, G.149, D.153, E.155 Ligands: MG.10, ANP.20 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain D Hydrogen bonds: B:T.194, B:K.195, B:Q.198, D:K.38, D:P.41, D:H.55, D:G.149, D:D.153, D:E.155 Salt bridges: B:K.193, B:K.193, B:K.195, B:K.195, B:K.229, B:K.229 Hydrophobic interactions: D:D.40 pi-Stacking: D:H.55

4 x GLN: GLUTAMINE(Non-covalent)

GLN.2: 15 residues within 4Å: Chain A: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, M.448, R.479, H.480, R.481, F.482, H.526 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.373, A:H.480 Hydrogen bonds: A:G.372, A:G.372, A:L.400, A:Q.403, A:R.481, A:F.482, Q.2 Salt bridges: A:R.481 GLN.7: 15 residues within 4Å: Chain B: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, M.448, R.479, H.480, R.481, F.482, H.526 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.373, B:H.480 Hydrogen bonds: B:G.372, B:G.372, B:L.400, B:Q.403, B:R.481, B:F.482, Q.7 Salt bridges: B:R.481 GLN.13: 15 residues within 4Å: Chain C: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, M.448, R.479, H.480, R.481, F.482, H.526 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.373, C:H.480 Hydrogen bonds: C:G.372, C:G.372, C:L.400, C:Q.403, C:R.481, C:F.482 Salt bridges: C:R.481 GLN.18: 15 residues within 4Å: Chain D: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, M.448, R.479, H.480, R.481, F.482, H.526 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:F.373, D:H.480 Hydrogen bonds: D:G.372, D:G.372, D:L.400, D:Q.403, D:R.481, D:F.482 Salt bridges: D:R.481

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.16, G.17, K.38, D.70, E.146 Ligands: ANP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.70, A:E.146 MG.5: 3 residues within 4Å: Chain A: K.193, K.229 Ligands: UTP.12 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain B: K.16, G.17, K.38, D.70, E.146 Ligands: ANP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.70, B:E.146 MG.10: 3 residues within 4Å: Chain B: K.193, K.229 Ligands: UTP.17 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: K.193, K.229 Ligands: UTP.1 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain C: K.16, G.17, K.38, D.70, E.146 Ligands: ANP.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.70, C:E.146 MG.16: 3 residues within 4Å: Chain D: K.193, K.229 Ligands: UTP.6 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain D: K.16, G.17, K.38, D.70, E.146 Ligands: ANP.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.70, D:E.146

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

ANP.4: 27 residues within 4Å: Chain A: S.12, G.13, I.14, G.15, K.16, G.17, I.18, K.38, D.68, L.69, D.70, N.73, E.146, G.148, G.149, R.217, V.244, H.245, D.246, V.247, I.250, V.253, L.256 Chain C: S.188, T.189 Ligands: UTP.1, MG.3 15 PLIP interactions: 1 interactions with chain C, 14 interactions with chain A Hydrogen bonds: C:S.188, A:G.13, A:I.14, A:G.15, A:K.16, A:K.16, A:G.17, A:I.18, A:K.38, A:D.70, A:E.146, A:G.149, A:H.245, A:V.247 pi-Cation interactions: A:R.217 ANP.9: 27 residues within 4Å: Chain B: S.12, G.13, I.14, G.15, K.16, G.17, I.18, K.38, D.68, L.69, D.70, N.73, E.146, G.148, G.149, R.217, V.244, H.245, D.246, V.247, I.250, V.253, L.256 Chain D: S.188, T.189 Ligands: UTP.6, MG.8 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.13, B:I.14, B:G.15, B:K.16, B:K.16, B:G.17, B:I.18, B:K.38, B:D.70, B:E.146, B:G.149, B:H.245, B:V.247, D:S.188 pi-Cation interactions: B:R.217 ANP.15: 27 residues within 4Å: Chain A: S.188, T.189 Chain C: S.12, G.13, I.14, G.15, K.16, G.17, I.18, K.38, D.68, L.69, D.70, N.73, E.146, G.148, G.149, R.217, V.244, H.245, D.246, V.247, I.250, V.253, L.256 Ligands: UTP.12, MG.14 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.13, C:I.14, C:G.15, C:K.16, C:K.16, C:G.17, C:I.18, C:K.38, C:D.70, C:E.146, C:G.149, C:H.245, C:V.247, A:S.188 pi-Cation interactions: C:R.217 ANP.20: 27 residues within 4Å: Chain B: S.188, T.189 Chain D: S.12, G.13, I.14, G.15, K.16, G.17, I.18, K.38, D.68, L.69, D.70, N.73, E.146, G.148, G.149, R.217, V.244, H.245, D.246, V.247, I.250, V.253, L.256 Ligands: UTP.17, MG.19 15 PLIP interactions: 1 interactions with chain B, 14 interactions with chain D Hydrogen bonds: B:S.188, D:G.13, D:I.14, D:G.15, D:K.16, D:K.16, D:G.17, D:I.18, D:K.38, D:D.70, D:E.146, D:G.149, D:H.245, D:V.247 pi-Cation interactions: D:R.217

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 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
O

C
P

D
Q

CTP synthase 1

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