SMTL ID : 7rmv.1

Yeast CTP Synthase (Ura7) H360R Filament bound to Substrates

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: H.187 Chain B: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Ligands: UTP.2 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B Salt bridges: A:H.187, B:K.16 Hydrogen bonds: B:G.13, B:G.15, B:K.16, B:G.17, B:V.18, B:D.70, B:R.215, B:R.215, B:V.242 pi-Cation interactions: B:R.215, B:R.215 ATP.3: 17 residues within 4Å: Chain A: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Chain B: H.187 Ligands: UTP.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.13, A:G.15, A:K.16, A:G.17, A:V.18, A:D.70, A:R.215, A:R.215, A:V.242 Salt bridges: A:K.16, B:H.187 pi-Cation interactions: A:R.215, A:R.215 ATP.5: 17 residues within 4Å: Chain C: H.187 Chain D: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Ligands: UTP.6 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.13, D:G.15, D:K.16, D:G.17, D:V.18, D:D.70, D:D.70, D:R.215, D:R.215, D:V.242 Salt bridges: D:K.16, C:H.187 pi-Cation interactions: D:R.215, D:R.215 ATP.7: 17 residues within 4Å: Chain C: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Chain D: H.187 Ligands: UTP.8 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.13, C:G.15, C:K.16, C:G.17, C:V.18, C:D.70, C:D.70, C:R.215, C:R.215, C:V.242 Salt bridges: C:K.16, D:H.187 pi-Cation interactions: C:R.215, C:R.215 ATP.9: 17 residues within 4Å: Chain E: H.187 Chain F: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Ligands: UTP.10 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.13, F:G.15, F:K.16, F:G.17, F:V.18, F:D.70, F:R.215, F:R.215, F:V.242 Salt bridges: F:K.16, E:H.187 pi-Cation interactions: F:R.215, F:R.215 ATP.11: 17 residues within 4Å: Chain E: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Chain F: H.187 Ligands: UTP.12 13 PLIP interactions: 1 interactions with chain F, 12 interactions with chain E Salt bridges: F:H.187, E:K.16 Hydrogen bonds: E:G.13, E:G.15, E:K.16, E:G.17, E:V.18, E:D.70, E:R.215, E:R.215, E:V.242 pi-Cation interactions: E:R.215, E:R.215 ATP.13: 17 residues within 4Å: Chain G: H.187 Chain H: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Ligands: UTP.14 14 PLIP interactions: 13 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:G.13, H:G.15, H:K.16, H:G.17, H:V.18, H:D.70, H:D.70, H:R.215, H:R.215, H:V.242 Salt bridges: H:K.16, G:H.187 pi-Cation interactions: H:R.215, H:R.215 ATP.15: 17 residues within 4Å: Chain G: G.13, I.14, G.15, K.16, G.17, V.18, K.38, D.70, E.146, R.215, V.242, H.243, D.244, T.248, V.251 Chain H: H.187 Ligands: UTP.16 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:G.13, G:G.15, G:K.16, G:G.17, G:V.18, G:D.70, G:D.70, G:R.215, G:R.215, G:V.242 Salt bridges: G:K.16, H:H.187 pi-Cation interactions: G:R.215, G:R.215

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

UTP.2: 22 residues within 4Å: Chain A: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain B: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain C: Q.112 Ligands: ATP.1 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:S.12, B:S.12, B:D.40, B:Y.42, B:G.149, A:E.189, A:T.192, A:T.192, A:K.193 Salt bridges: A:K.191, A:K.191, A:K.193, A:K.193, A:K.227 UTP.4: 22 residues within 4Å: Chain A: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain B: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain D: Q.112 Ligands: ATP.3 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.189, B:T.192, B:T.192, B:K.193, A:S.12, A:S.12, A:D.40, A:Y.42, A:G.149 Salt bridges: B:K.191, B:K.191, B:K.193, B:K.193, B:K.227 UTP.6: 22 residues within 4Å: Chain A: Q.112 Chain C: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain D: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Ligands: ATP.5 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:S.12, D:S.12, D:S.12, D:D.40, D:D.40, D:Y.42, D:G.149, C:E.189, C:T.192, C:T.192, C:K.193 Salt bridges: C:K.191, C:K.191, C:K.193, C:K.193, C:K.227 UTP.8: 22 residues within 4Å: Chain B: Q.112 Chain C: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain D: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Ligands: ATP.7 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:E.189, D:T.192, D:T.192, D:K.193, C:S.12, C:S.12, C:S.12, C:D.40, C:D.40, C:Y.42, C:G.149 Salt bridges: D:K.191, D:K.191, D:K.193, D:K.193, D:K.227 UTP.10: 22 residues within 4Å: Chain E: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain F: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain G: Q.112 Ligands: ATP.9 14 PLIP interactions: 5 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:S.12, F:S.12, F:D.40, F:Y.42, F:G.149, E:E.189, E:T.192, E:T.192, E:K.193 Salt bridges: E:K.191, E:K.191, E:K.193, E:K.193, E:K.227 UTP.12: 22 residues within 4Å: Chain E: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain F: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain H: Q.112 Ligands: ATP.11 14 PLIP interactions: 5 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:S.12, E:S.12, E:D.40, E:Y.42, E:G.149, F:E.189, F:T.192, F:T.192, F:K.193 Salt bridges: F:K.191, F:K.191, F:K.193, F:K.193, F:K.227 UTP.14: 22 residues within 4Å: Chain E: Q.112 Chain G: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Chain H: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Ligands: ATP.13 16 PLIP interactions: 9 interactions with chain G, 7 interactions with chain H Hydrogen bonds: G:E.189, G:T.192, G:T.192, G:K.193, H:S.12, H:S.12, H:S.12, H:D.40, H:D.40, H:Y.42, H:G.149 Salt bridges: G:K.191, G:K.191, G:K.193, G:K.193, G:K.227 UTP.16: 22 residues within 4Å: Chain F: Q.112 Chain G: I.11, S.12, G.13, K.38, D.40, P.41, Y.42, G.148, G.149, T.150, D.153, E.155 Chain H: E.189, Q.190, K.191, T.192, K.193, P.194, Q.196, K.227 Ligands: ATP.15 16 PLIP interactions: 7 interactions with chain G, 9 interactions with chain H Hydrogen bonds: G:S.12, G:S.12, G:S.12, G:D.40, G:D.40, G:Y.42, G:G.149, H:E.189, H:T.192, H:T.192, H:K.193 Salt bridges: H:K.191, H:K.191, H:K.193, H:K.193, H:K.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hansen, J.M. et al., Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. Elife (2021)

Release Date

2021-11-24

Peptides

CTP synthase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

CTP synthase