SMTL ID : 5u03.3 (2 other biounits)

Cryo-EM structure of the human CTP synthase filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: G.13, I.14, G.15, K.16, G.17, I.18, D.70, E.146, R.217, V.244, H.245, D.246, V.247, I.250, D.312 Ligands: UTP.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.13, A:I.14, A:G.15, A:K.16, A:G.17, A:I.18, A:D.70, A:R.217, A:R.217, A:H.245, A:D.246, A:V.247, A:D.312 pi-Cation interactions: A:R.217 ATP.3: 16 residues within 4Å: Chain B: G.13, I.14, G.15, K.16, G.17, I.18, D.70, E.146, R.217, V.244, H.245, D.246, V.247, I.250, D.312 Ligands: UTP.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.13, B:I.14, B:G.15, B:K.16, B:G.17, B:I.18, B:D.70, B:R.217, B:R.217, B:H.245, B:D.246, B:V.247, B:D.312 pi-Cation interactions: B:R.217 ATP.5: 16 residues within 4Å: Chain C: G.13, I.14, G.15, K.16, G.17, I.18, D.70, E.146, R.217, V.244, H.245, D.246, V.247, I.250, D.312 Ligands: UTP.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.13, C:I.14, C:G.15, C:K.16, C:G.17, C:I.18, C:D.70, C:E.146, C:E.146, C:R.217, C:R.217, C:H.245, C:V.247, C:D.312 pi-Cation interactions: C:R.217 ATP.7: 16 residues within 4Å: Chain D: G.13, I.14, G.15, K.16, G.17, I.18, D.70, E.146, R.217, V.244, H.245, D.246, V.247, I.250, D.312 Ligands: UTP.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.13, D:I.14, D:G.15, D:K.16, D:G.17, D:I.18, D:D.70, D:E.146, D:E.146, D:R.217, D:R.217, D:H.245, D:V.247, D:D.312 pi-Cation interactions: D:R.217

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

UTP.2: 16 residues within 4Å: Chain A: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain B: K.193, T.194, K.195, Q.198, F.233 Chain C: Q.112 Ligands: ATP.1 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.194, B:K.195, B:Q.198, A:S.12, A:K.38, A:D.40, A:Y.42 Salt bridges: B:K.193 UTP.4: 16 residues within 4Å: Chain A: K.193, T.194, K.195, Q.198, F.233 Chain B: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain D: Q.112 Ligands: ATP.3 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.12, B:K.38, B:D.40, B:Y.42, A:T.194, A:K.195, A:Q.198, D:Q.112 Salt bridges: A:K.193 UTP.6: 16 residues within 4Å: Chain A: Q.112 Chain C: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain D: K.193, T.194, K.195, Q.198, F.233 Ligands: ATP.5 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:T.194, D:T.194, D:K.195, D:Q.198, C:S.12, C:K.38, C:D.40, C:D.40, C:Y.42, C:Y.42, C:E.146 Salt bridges: D:K.193 UTP.8: 16 residues within 4Å: Chain B: Q.112 Chain C: K.193, T.194, K.195, Q.198, F.233 Chain D: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Ligands: ATP.7 13 PLIP interactions: 5 interactions with chain C, 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.194, C:T.194, C:K.195, C:Q.198, D:S.12, D:K.38, D:D.40, D:D.40, D:Y.42, D:Y.42, D:E.146, B:Q.112 Salt bridges: C:K.193

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 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP synthase 1

Related Entries With Identical Sequence