SMTL ID : 7rl0.1

Yeast CTP Synthase (URA8) Filament bound to ATP/UTP at low pH

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: G.17, K.38, D.70, E.146 Ligands: ATP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.70, A:D.70, A:E.146 MG.3: 2 residues within 4Å: Chain A: K.227 Ligands: UTP.4 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: G.17, K.38, D.70, E.146 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.70, B:D.70, B:E.146 MG.7: 2 residues within 4Å: Chain B: K.227 Ligands: UTP.8 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain C: G.17, K.38, D.70, E.146 Ligands: ATP.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.70, C:D.70, C:E.146 MG.10: 2 residues within 4Å: Chain C: K.227 Ligands: UTP.11 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: K.227 Ligands: UTP.14 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain D: G.17, K.38, D.70, E.146 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.70, D:D.70, D:E.146 MG.17: 5 residues within 4Å: Chain E: G.17, K.38, D.70, E.146 Ligands: ATP.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.70, E:D.70, E:E.146 MG.19: 2 residues within 4Å: Chain E: K.227 Ligands: UTP.20 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain F: G.17, K.38, D.70, E.146 Ligands: ATP.21 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.70, F:D.70, F:E.146 MG.23: 2 residues within 4Å: Chain F: K.227 Ligands: UTP.24 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain G: K.227 Ligands: UTP.26 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain G: G.17, K.38, D.70, E.146 Ligands: ATP.27 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.70, G:D.70, G:E.146 MG.29: 2 residues within 4Å: Chain H: K.227 Ligands: UTP.30 No protein-ligand interaction detected (PLIP) MG.32: 5 residues within 4Å: Chain H: G.17, K.38, D.70, E.146 Ligands: ATP.31 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.70, H:D.70, H:E.146 MG.33: 5 residues within 4Å: Chain I: G.17, K.38, D.70, E.146 Ligands: ATP.34 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.70, I:D.70, I:E.146 MG.35: 2 residues within 4Å: Chain I: K.227 Ligands: UTP.36 No protein-ligand interaction detected (PLIP) MG.38: 5 residues within 4Å: Chain J: G.17, K.38, D.70, E.146 Ligands: ATP.37 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.70, J:D.70, J:E.146 MG.39: 2 residues within 4Å: Chain J: K.227 Ligands: UTP.40 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain K: K.227 Ligands: UTP.42 No protein-ligand interaction detected (PLIP) MG.44: 5 residues within 4Å: Chain K: G.17, K.38, D.70, E.146 Ligands: ATP.43 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.70, K:D.70, K:E.146 MG.45: 2 residues within 4Å: Chain L: K.227 Ligands: UTP.46 No protein-ligand interaction detected (PLIP) MG.48: 5 residues within 4Å: Chain L: G.17, K.38, D.70, E.146 Ligands: ATP.47 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.70, L:D.70, L:E.146

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

ATP.2: 18 residues within 4Å: Chain A: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain D: H.187 Ligands: MG.1, UTP.14 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.13, A:I.14, A:G.15, A:K.16, A:G.17, A:V.18, A:H.243, A:V.245, D:H.187 Salt bridges: A:K.16 pi-Cation interactions: A:R.215 ATP.6: 18 residues within 4Å: Chain B: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain C: H.187 Ligands: MG.5, UTP.11 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.13, B:I.14, B:G.15, B:K.16, B:G.17, B:V.18, B:H.243, B:V.245, C:H.187 Salt bridges: B:K.16 pi-Cation interactions: B:R.215 ATP.12: 18 residues within 4Å: Chain B: H.187 Chain C: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.8, MG.9 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.13, C:I.14, C:G.15, C:K.16, C:G.17, C:V.18, C:H.243, C:V.245, B:H.187 Salt bridges: C:K.16 pi-Cation interactions: C:R.215 ATP.15: 18 residues within 4Å: Chain A: H.187 Chain D: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.4, MG.16 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain D Hydrogen bonds: A:H.187, D:G.13, D:I.14, D:G.15, D:K.16, D:G.17, D:V.18, D:H.243, D:V.245 Salt bridges: D:K.16 pi-Cation interactions: D:R.215 ATP.18: 18 residues within 4Å: Chain E: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain H: H.187 Ligands: MG.17, UTP.30 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:G.17, E:V.18, E:H.243, E:V.245, H:H.187 Salt bridges: E:K.16 pi-Cation interactions: E:R.215 ATP.21: 18 residues within 4Å: Chain F: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain G: H.187 Ligands: MG.22, UTP.26 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:G.13, F:I.14, F:G.15, F:K.16, F:G.17, F:V.18, F:H.243, F:V.245, G:H.187 Salt bridges: F:K.16 pi-Cation interactions: F:R.215 ATP.27: 18 residues within 4Å: Chain F: H.187 Chain G: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.24, MG.28 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:G.13, G:I.14, G:G.15, G:K.16, G:G.17, G:V.18, G:H.243, G:V.245, F:H.187 Salt bridges: G:K.16 pi-Cation interactions: G:R.215 ATP.31: 18 residues within 4Å: Chain E: H.187 Chain H: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.20, MG.32 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:G.13, H:I.14, H:G.15, H:K.16, H:G.17, H:V.18, H:H.243, H:V.245, E:H.187 Salt bridges: H:K.16 pi-Cation interactions: H:R.215 ATP.34: 18 residues within 4Å: Chain I: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain L: H.187 Ligands: MG.33, UTP.46 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:G.13, I:I.14, I:G.15, I:K.16, I:G.17, I:V.18, I:H.243, I:V.245, L:H.187 Salt bridges: I:K.16 pi-Cation interactions: I:R.215 ATP.37: 18 residues within 4Å: Chain J: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Chain K: H.187 Ligands: MG.38, UTP.42 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:G.13, J:I.14, J:G.15, J:K.16, J:G.17, J:V.18, J:H.243, J:V.245, K:H.187 Salt bridges: J:K.16 pi-Cation interactions: J:R.215 ATP.43: 18 residues within 4Å: Chain J: H.187 Chain K: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.40, MG.44 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:G.13, K:I.14, K:G.15, K:K.16, K:G.17, K:V.18, K:H.243, K:V.245, J:H.187 Salt bridges: K:K.16 pi-Cation interactions: K:R.215 ATP.47: 18 residues within 4Å: Chain I: H.187 Chain L: G.13, I.14, G.15, K.16, G.17, V.18, D.70, E.146, R.215, V.242, H.243, D.244, V.245, T.248, V.251 Ligands: UTP.36, MG.48 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain I Hydrogen bonds: L:G.13, L:I.14, L:G.15, L:K.16, L:G.17, L:V.18, L:H.243, L:V.245, I:H.187 Salt bridges: L:K.16 pi-Cation interactions: L:R.215

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

UTP.4: 22 residues within 4Å: Chain A: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain C: T.110, Q.112 Chain D: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Ligands: MG.3, ATP.15 19 PLIP interactions: 9 interactions with chain A, 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:T.192, A:T.192, A:K.193, A:K.193, D:S.12, D:S.12, D:D.40, D:D.40, D:H.55, D:G.149, D:E.155, C:Q.112, C:Q.112 Salt bridges: A:K.191, A:K.193, A:K.193, A:K.227, A:K.227 pi-Stacking: D:H.55 UTP.8: 22 residues within 4Å: Chain B: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain C: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain D: T.110, Q.112 Ligands: MG.7, ATP.12 18 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C, 8 interactions with chain B Hydrogen bonds: D:Q.112, D:Q.112, C:S.12, C:S.12, C:D.40, C:H.55, C:G.149, C:E.155, C:E.155, B:T.192, B:K.193, B:K.193 pi-Stacking: C:H.55 Salt bridges: B:K.191, B:K.193, B:K.193, B:K.227, B:K.227 UTP.11: 22 residues within 4Å: Chain A: T.110, Q.112 Chain B: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain C: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.6, MG.10 18 PLIP interactions: 8 interactions with chain C, 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:T.192, C:K.193, C:K.193, B:S.12, B:S.12, B:D.40, B:H.55, B:G.149, B:E.155, B:E.155, A:Q.112, A:Q.112 Salt bridges: C:K.191, C:K.193, C:K.193, C:K.227, C:K.227 pi-Stacking: B:H.55 UTP.14: 22 residues within 4Å: Chain A: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain B: T.110, Q.112 Chain D: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.2, MG.13 19 PLIP interactions: 2 interactions with chain B, 9 interactions with chain D, 8 interactions with chain A Hydrogen bonds: B:Q.112, B:Q.112, D:T.192, D:T.192, D:K.193, D:K.193, A:S.12, A:S.12, A:D.40, A:D.40, A:H.55, A:G.149, A:E.155 Salt bridges: D:K.191, D:K.193, D:K.193, D:K.227, D:K.227 pi-Stacking: A:H.55 UTP.20: 22 residues within 4Å: Chain E: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain G: T.110, Q.112 Chain H: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Ligands: MG.19, ATP.31 19 PLIP interactions: 8 interactions with chain H, 9 interactions with chain E, 2 interactions with chain G Hydrogen bonds: H:S.12, H:S.12, H:D.40, H:D.40, H:H.55, H:G.149, H:E.155, E:T.192, E:T.192, E:K.193, E:K.193, G:Q.112, G:Q.112 pi-Stacking: H:H.55 Salt bridges: E:K.191, E:K.193, E:K.193, E:K.227, E:K.227 UTP.24: 22 residues within 4Å: Chain F: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain G: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain H: T.110, Q.112 Ligands: MG.23, ATP.27 18 PLIP interactions: 8 interactions with chain F, 2 interactions with chain H, 8 interactions with chain G Hydrogen bonds: F:T.192, F:K.193, F:K.193, H:Q.112, H:Q.112, G:S.12, G:S.12, G:D.40, G:H.55, G:G.149, G:E.155, G:E.155 Salt bridges: F:K.191, F:K.193, F:K.193, F:K.227, F:K.227 pi-Stacking: G:H.55 UTP.26: 22 residues within 4Å: Chain E: T.110, Q.112 Chain F: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain G: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.21, MG.25 17 PLIP interactions: 8 interactions with chain G, 7 interactions with chain F, 2 interactions with chain E Hydrogen bonds: G:T.192, G:K.193, G:K.193, F:S.12, F:S.12, F:D.40, F:G.149, F:E.155, F:E.155, E:Q.112, E:Q.112 Salt bridges: G:K.191, G:K.193, G:K.193, G:K.227, G:K.227 pi-Stacking: F:H.55 UTP.30: 22 residues within 4Å: Chain E: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain F: T.110, Q.112 Chain H: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.18, MG.29 19 PLIP interactions: 8 interactions with chain E, 9 interactions with chain H, 2 interactions with chain F Hydrogen bonds: E:S.12, E:S.12, E:D.40, E:D.40, E:H.55, E:G.149, E:E.155, H:T.192, H:T.192, H:K.193, H:K.193, F:Q.112, F:Q.112 pi-Stacking: E:H.55 Salt bridges: H:K.191, H:K.193, H:K.193, H:K.227, H:K.227 UTP.36: 22 residues within 4Å: Chain I: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain K: T.110, Q.112 Chain L: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Ligands: MG.35, ATP.47 19 PLIP interactions: 8 interactions with chain L, 9 interactions with chain I, 2 interactions with chain K Hydrogen bonds: L:S.12, L:S.12, L:D.40, L:D.40, L:H.55, L:G.149, L:E.155, I:T.192, I:T.192, I:K.193, I:K.193, K:Q.112, K:Q.112 pi-Stacking: L:H.55 Salt bridges: I:K.191, I:K.193, I:K.193, I:K.227, I:K.227 UTP.40: 22 residues within 4Å: Chain J: Q.190, K.191, T.192, K.193, Q.196, K.227 Chain K: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain L: T.110, Q.112 Ligands: MG.39, ATP.43 18 PLIP interactions: 8 interactions with chain J, 8 interactions with chain K, 2 interactions with chain L Hydrogen bonds: J:T.192, J:K.193, J:K.193, K:S.12, K:S.12, K:D.40, K:H.55, K:G.149, K:E.155, K:E.155, L:Q.112, L:Q.112 Salt bridges: J:K.191, J:K.193, J:K.193, J:K.227, J:K.227 pi-Stacking: K:H.55 UTP.42: 22 residues within 4Å: Chain I: T.110, Q.112 Chain J: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain K: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.37, MG.41 18 PLIP interactions: 8 interactions with chain J, 8 interactions with chain K, 2 interactions with chain I Hydrogen bonds: J:S.12, J:S.12, J:D.40, J:H.55, J:G.149, J:E.155, J:E.155, K:T.192, K:K.193, K:K.193, I:Q.112, I:Q.112 pi-Stacking: J:H.55 Salt bridges: K:K.191, K:K.193, K:K.193, K:K.227, K:K.227 UTP.46: 22 residues within 4Å: Chain I: S.12, G.13, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, E.155 Chain J: T.110, Q.112 Chain L: Q.190, K.191, T.192, K.193, Q.196, K.227 Ligands: ATP.34, MG.45 19 PLIP interactions: 8 interactions with chain I, 9 interactions with chain L, 2 interactions with chain J Hydrogen bonds: I:S.12, I:S.12, I:D.40, I:D.40, I:H.55, I:G.149, I:E.155, L:T.192, L:T.192, L:K.193, L:K.193, J:Q.112, J:Q.112 pi-Stacking: I:H.55 Salt bridges: L:K.191, L:K.193, L:K.193, L:K.227, L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
W

J
X

K
Y

L
Z

CTP synthase

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