SMTL ID : 7rmc.1

Yeast CTP Synthase (Ura7) filament bound to CTP at low pH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

CTP.1: 13 residues within 4Å: Chain A: S.12, D.153, I.154, E.155 Chain B: K.191, T.192, K.193, Q.196, K.227, F.231 Chain D: Q.112, I.113, V.114 17 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:F.231 Hydrogen bonds: B:T.192, B:K.193, B:Q.196, A:S.12, A:D.153, A:I.154, A:E.155, A:E.155, D:Q.112, D:Q.112, D:I.113 Salt bridges: B:K.191, B:K.193, B:K.193, B:K.227, B:K.227 CTP.2: 13 residues within 4Å: Chain A: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain B: H.187 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.73 Hydrogen bonds: A:G.13, A:G.15, A:K.16, A:G.17, A:V.18, A:N.73, A:N.73, A:Y.77 Salt bridges: A:K.16 CTP.3: 13 residues within 4Å: Chain A: K.191, T.192, K.193, Q.196, K.227, F.231 Chain B: S.12, D.153, I.154, E.155 Chain C: Q.112, I.113, V.114 16 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:F.231 Hydrogen bonds: A:T.192, A:K.193, A:Q.196, B:S.12, B:S.12, B:I.154, B:E.155, C:Q.112, C:Q.112, C:I.113 Salt bridges: A:K.193, A:K.193, A:K.193, A:K.227, A:K.227 CTP.4: 13 residues within 4Å: Chain A: H.187 Chain B: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.73 Hydrogen bonds: B:G.13, B:G.15, B:K.16, B:G.17, B:V.18, B:D.70, B:N.73, B:N.73, B:Y.77 Salt bridges: B:K.16 CTP.5: 13 residues within 4Å: Chain B: Q.112, I.113, V.114 Chain C: S.12, D.153, I.154, E.155 Chain D: K.191, T.192, K.193, Q.196, K.227, F.231 17 PLIP interactions: 10 interactions with chain D, 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: D:F.231 Hydrogen bonds: D:T.192, D:T.192, D:K.193, D:Q.196, B:Q.112, B:Q.112, B:I.113, C:S.12, C:S.12, C:I.154, C:E.155 Salt bridges: D:K.191, D:K.193, D:K.193, D:K.227, D:K.227 CTP.6: 13 residues within 4Å: Chain C: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain D: H.187 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.73 Hydrogen bonds: C:G.13, C:G.15, C:K.16, C:G.17, C:V.18, C:D.70, C:N.73, C:N.73, C:Y.77 Salt bridges: C:K.16 CTP.7: 13 residues within 4Å: Chain A: Q.112, I.113, V.114 Chain C: K.191, T.192, K.193, Q.196, K.227, F.231 Chain D: S.12, D.153, I.154, E.155 17 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A, 9 interactions with chain C Hydrogen bonds: D:S.12, D:D.153, D:I.154, D:E.155, D:E.155, A:Q.112, A:Q.112, A:I.113, C:T.192, C:K.193, C:Q.196 Hydrophobic interactions: C:F.231 Salt bridges: C:K.193, C:K.193, C:K.193, C:K.227, C:K.227 CTP.8: 13 residues within 4Å: Chain C: H.187 Chain D: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:N.73 Hydrogen bonds: D:G.13, D:G.15, D:K.16, D:G.17, D:V.18, D:N.73, D:N.73, D:Y.77 Salt bridges: D:K.16 CTP.9: 13 residues within 4Å: Chain E: S.12, D.153, I.154, E.155 Chain F: K.191, T.192, K.193, Q.196, K.227, F.231 Chain H: Q.112, I.113, V.114 17 PLIP interactions: 9 interactions with chain F, 5 interactions with chain E, 3 interactions with chain H Hydrophobic interactions: F:F.231 Hydrogen bonds: F:T.192, F:K.193, F:Q.196, E:S.12, E:D.153, E:I.154, E:E.155, E:E.155, H:Q.112, H:Q.112, H:I.113 Salt bridges: F:K.191, F:K.193, F:K.193, F:K.227, F:K.227 CTP.10: 13 residues within 4Å: Chain E: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain F: H.187 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:N.73 Hydrogen bonds: E:G.13, E:G.15, E:K.16, E:G.17, E:V.18, E:N.73, E:N.73, E:Y.77 Salt bridges: E:K.16 CTP.11: 13 residues within 4Å: Chain E: K.191, T.192, K.193, Q.196, K.227, F.231 Chain F: S.12, D.153, I.154, E.155 Chain G: Q.112, I.113, V.114 17 PLIP interactions: 10 interactions with chain E, 4 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: E:F.231 Hydrogen bonds: E:T.192, E:T.192, E:K.193, E:Q.196, F:S.12, F:S.12, F:I.154, F:E.155, G:Q.112, G:Q.112, G:I.113 Salt bridges: E:K.193, E:K.193, E:K.193, E:K.227, E:K.227 CTP.12: 13 residues within 4Å: Chain E: H.187 Chain F: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:N.73 Hydrogen bonds: F:G.13, F:G.15, F:K.16, F:G.17, F:V.18, F:D.70, F:N.73, F:N.73, F:Y.77 Salt bridges: F:K.16 CTP.13: 13 residues within 4Å: Chain F: Q.112, I.113, V.114 Chain G: S.12, D.153, I.154, E.155 Chain H: K.191, T.192, K.193, Q.196, K.227, F.231 16 PLIP interactions: 9 interactions with chain H, 3 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: H:F.231 Hydrogen bonds: H:T.192, H:K.193, H:Q.196, F:Q.112, F:Q.112, F:I.113, G:S.12, G:S.12, G:I.154, G:E.155 Salt bridges: H:K.191, H:K.193, H:K.193, H:K.227, H:K.227 CTP.14: 13 residues within 4Å: Chain G: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain H: H.187 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:N.73 Hydrogen bonds: G:G.13, G:G.15, G:K.16, G:G.17, G:V.18, G:D.70, G:N.73, G:N.73, G:Y.77 Salt bridges: G:K.16 CTP.15: 13 residues within 4Å: Chain E: Q.112, I.113, V.114 Chain G: K.191, T.192, K.193, Q.196, K.227, F.231 Chain H: S.12, D.153, I.154, E.155 17 PLIP interactions: 9 interactions with chain G, 3 interactions with chain E, 5 interactions with chain H Hydrophobic interactions: G:F.231 Hydrogen bonds: G:T.192, G:K.193, G:Q.196, E:Q.112, E:Q.112, E:I.113, H:S.12, H:D.153, H:I.154, H:E.155, H:E.155 Salt bridges: G:K.193, G:K.193, G:K.193, G:K.227, G:K.227 CTP.16: 13 residues within 4Å: Chain G: H.187 Chain H: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:N.73 Hydrogen bonds: H:G.13, H:G.15, H:K.16, H:G.17, H:V.18, H:N.73, H:N.73, H:Y.77 Salt bridges: H:K.16 CTP.17: 13 residues within 4Å: Chain I: S.12, D.153, I.154, E.155 Chain J: K.191, T.192, K.193, Q.196, K.227, F.231 Chain L: Q.112, I.113, V.114 17 PLIP interactions: 5 interactions with chain I, 9 interactions with chain J, 3 interactions with chain L Hydrogen bonds: I:S.12, I:D.153, I:I.154, I:E.155, I:E.155, J:T.192, J:K.193, J:Q.196, L:Q.112, L:Q.112, L:I.113 Hydrophobic interactions: J:F.231 Salt bridges: J:K.191, J:K.193, J:K.193, J:K.227, J:K.227 CTP.18: 13 residues within 4Å: Chain I: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain J: H.187 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:N.73 Hydrogen bonds: I:G.13, I:G.15, I:K.16, I:G.17, I:V.18, I:N.73, I:N.73, I:Y.77 Salt bridges: I:K.16 CTP.19: 13 residues within 4Å: Chain I: K.191, T.192, K.193, Q.196, K.227, F.231 Chain J: S.12, D.153, I.154, E.155 Chain K: Q.112, I.113, V.114 17 PLIP interactions: 4 interactions with chain J, 10 interactions with chain I, 3 interactions with chain K Hydrogen bonds: J:S.12, J:S.12, J:I.154, J:E.155, I:T.192, I:T.192, I:K.193, I:Q.196, K:Q.112, K:Q.112, K:I.113 Hydrophobic interactions: I:F.231 Salt bridges: I:K.193, I:K.193, I:K.193, I:K.227, I:K.227 CTP.20: 13 residues within 4Å: Chain I: H.187 Chain J: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:N.73 Hydrogen bonds: J:G.13, J:G.15, J:K.16, J:G.17, J:V.18, J:D.70, J:N.73, J:N.73, J:Y.77 Salt bridges: J:K.16 CTP.21: 13 residues within 4Å: Chain J: Q.112, I.113, V.114 Chain K: S.12, D.153, I.154, E.155 Chain L: K.191, T.192, K.193, Q.196, K.227, F.231 17 PLIP interactions: 3 interactions with chain J, 10 interactions with chain L, 4 interactions with chain K Hydrogen bonds: J:Q.112, J:Q.112, J:I.113, L:T.192, L:T.192, L:K.193, L:Q.196, K:S.12, K:S.12, K:I.154, K:E.155 Hydrophobic interactions: L:F.231 Salt bridges: L:K.191, L:K.193, L:K.193, L:K.227, L:K.227 CTP.22: 13 residues within 4Å: Chain K: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 Chain L: H.187 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:N.73 Hydrogen bonds: K:G.13, K:G.15, K:K.16, K:G.17, K:V.18, K:D.70, K:N.73, K:N.73, K:Y.77 Salt bridges: K:K.16 CTP.23: 13 residues within 4Å: Chain I: Q.112, I.113, V.114 Chain K: K.191, T.192, K.193, Q.196, K.227, F.231 Chain L: S.12, D.153, I.154, E.155 17 PLIP interactions: 9 interactions with chain K, 5 interactions with chain L, 3 interactions with chain I Hydrophobic interactions: K:F.231 Hydrogen bonds: K:T.192, K:K.193, K:Q.196, L:S.12, L:D.153, L:I.154, L:E.155, L:E.155, I:Q.112, I:Q.112, I:I.113 Salt bridges: K:K.193, K:K.193, K:K.193, K:K.227, K:K.227 CTP.24: 13 residues within 4Å: Chain K: H.187 Chain L: G.13, I.14, G.15, K.16, G.17, V.18, D.70, N.73, Y.77, T.248, L.320, K.324 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:N.73 Hydrogen bonds: L:G.13, L:G.15, L:K.16, L:G.17, L:V.18, L:N.73, L:N.73, L:Y.77 Salt bridges: L:K.16

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 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
D

C
E

D
F

E
g

F
Q

G
S

H
U

I
h

J
R

K
T

L
W

CTP synthase 1