SMTL ID : 6pk4.1

cryoEM structure of the substrate-bound human CTP synthase 2 filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Covalent)

UTP.1: 14 residues within 4Å: Chain A: S.12, K.38, Y.42, H.55, D.70, G.149, T.150 Chain B: K.193, T.194, K.195, K.229, F.233 Chain C: Q.112 Ligands: ATP.2 9 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 5 interactions with chain B Hydrogen bonds: A:S.12, A:K.38, A:H.55, C:Q.112, B:T.194 Salt bridges: B:K.193, B:K.193, B:K.229, B:K.229 UTP.3: 14 residues within 4Å: Chain A: K.193, T.194, K.195, K.229, F.233 Chain B: S.12, K.38, Y.42, H.55, D.70, G.149, T.150 Chain D: Q.112 Ligands: ATP.4 9 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:T.194, B:S.12, B:K.38, B:H.55, D:Q.112 Salt bridges: A:K.193, A:K.193, A:K.229, A:K.229 UTP.5: 14 residues within 4Å: Chain A: Q.112 Chain C: S.12, K.38, Y.42, H.55, D.70, G.149, T.150 Chain D: K.193, T.194, K.195, K.229, F.233 Ligands: ATP.6 8 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:Q.112, D:T.194, C:S.12, C:K.38 Salt bridges: D:K.193, D:K.193, D:K.229, D:K.229 UTP.7: 14 residues within 4Å: Chain B: Q.112 Chain C: K.193, T.194, K.195, K.229, F.233 Chain D: S.12, K.38, Y.42, H.55, D.70, G.149, T.150 Ligands: ATP.8 8 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.194, D:S.12, D:K.38, B:Q.112 Salt bridges: C:K.193, C:K.193, C:K.229, C:K.229

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.2: 13 residues within 4Å: Chain A: G.15, K.16, G.17, I.18, K.38, D.70, N.73, E.146, R.217, V.253, D.312 Chain B: T.189 Ligands: UTP.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.16, A:G.17, A:I.18, A:D.70, A:N.73, A:E.146, A:R.217, A:D.312 Salt bridges: A:K.38, A:K.38, A:H.55 pi-Cation interactions: A:R.217 ATP.4: 13 residues within 4Å: Chain A: T.189 Chain B: G.15, K.16, G.17, I.18, K.38, D.70, N.73, E.146, R.217, V.253, D.312 Ligands: UTP.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.16, B:G.17, B:I.18, B:D.70, B:N.73, B:E.146, B:R.217, B:D.312 Salt bridges: B:K.38, B:K.38, B:H.55 pi-Cation interactions: B:R.217 ATP.6: 13 residues within 4Å: Chain C: G.15, K.16, G.17, I.18, K.38, D.70, N.73, E.146, R.217, V.253, D.312 Chain D: T.189 Ligands: UTP.5 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.16, C:G.17, C:I.18, C:D.70, C:N.73, C:E.146, C:R.217 Salt bridges: C:K.38, C:K.38, C:H.55 pi-Cation interactions: C:R.217 ATP.8: 13 residues within 4Å: Chain C: T.189 Chain D: G.15, K.16, G.17, I.18, K.38, D.70, N.73, E.146, R.217, V.253, D.312 Ligands: UTP.7 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.16, D:G.17, D:I.18, D:D.70, D:N.73, D:E.146, D:R.217 Salt bridges: D:K.38, D:K.38, D:H.55 pi-Cation interactions: D:R.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments. Nat.Struct.Mol.Biol. (2020)

Release Date

2019-12-25

Peptides

CTP synthase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP synthase 2

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