SMTL ID : 5u03.1 (2 other biounits)

Cryo-EM structure of the human CTP synthase filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

16 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 ATP.9: 16 residues within 4Å: Chain E: 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.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:G.17, E:I.18, E:D.70, E:R.217, E:R.217, E:H.245, E:D.246, E:V.247, E:D.312 pi-Cation interactions: E:R.217 ATP.11: 16 residues within 4Å: Chain F: 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.12 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.13, F:I.14, F:G.15, F:K.16, F:G.17, F:I.18, F:D.70, F:R.217, F:R.217, F:H.245, F:D.246, F:V.247, F:D.312 pi-Cation interactions: F:R.217 ATP.13: 16 residues within 4Å: Chain G: 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.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.13, G:I.14, G:G.15, G:K.16, G:G.17, G:I.18, G:D.70, G:E.146, G:E.146, G:R.217, G:R.217, G:H.245, G:V.247, G:D.312 pi-Cation interactions: G:R.217 ATP.15: 16 residues within 4Å: Chain H: 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.16 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.13, H:I.14, H:G.15, H:K.16, H:G.17, H:I.18, H:D.70, H:E.146, H:E.146, H:R.217, H:R.217, H:H.245, H:V.247, H:D.312 pi-Cation interactions: H:R.217 ATP.17: 16 residues within 4Å: Chain I: 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.18 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:G.13, I:I.14, I:G.15, I:K.16, I:G.17, I:I.18, I:D.70, I:R.217, I:R.217, I:H.245, I:D.246, I:V.247, I:D.312 pi-Cation interactions: I:R.217 ATP.19: 16 residues within 4Å: Chain J: 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.20 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.13, J:I.14, J:G.15, J:K.16, J:G.17, J:I.18, J:D.70, J:R.217, J:R.217, J:H.245, J:D.246, J:V.247, J:D.312 pi-Cation interactions: J:R.217 ATP.21: 16 residues within 4Å: Chain K: 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.22 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.13, K:I.14, K:G.15, K:K.16, K:G.17, K:I.18, K:D.70, K:E.146, K:E.146, K:R.217, K:R.217, K:H.245, K:V.247, K:D.312 pi-Cation interactions: K:R.217 ATP.23: 16 residues within 4Å: Chain L: 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.24 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:G.13, L:I.14, L:G.15, L:K.16, L:G.17, L:I.18, L:D.70, L:E.146, L:E.146, L:R.217, L:R.217, L:H.245, L:V.247, L:D.312 pi-Cation interactions: L:R.217 ATP.25: 16 residues within 4Å: Chain M: 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.26 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:G.13, M:I.14, M:G.15, M:K.16, M:G.17, M:I.18, M:D.70, M:R.217, M:R.217, M:H.245, M:D.246, M:V.247, M:D.312 pi-Cation interactions: M:R.217 ATP.27: 16 residues within 4Å: Chain N: 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.28 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:G.13, N:I.14, N:G.15, N:K.16, N:G.17, N:I.18, N:D.70, N:R.217, N:R.217, N:H.245, N:D.246, N:V.247, N:D.312 pi-Cation interactions: N:R.217 ATP.29: 16 residues within 4Å: Chain O: 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.30 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: O:G.13, O:I.14, O:G.15, O:K.16, O:G.17, O:I.18, O:D.70, O:E.146, O:E.146, O:R.217, O:R.217, O:H.245, O:V.247, O:D.312 pi-Cation interactions: O:R.217 ATP.31: 16 residues within 4Å: Chain P: 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.32 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:G.13, P:I.14, P:G.15, P:K.16, P:G.17, P:I.18, P:D.70, P:E.146, P:E.146, P:R.217, P:R.217, P:H.245, P:V.247, P:D.312 pi-Cation interactions: P:R.217

16 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 A, 4 interactions with chain B Hydrogen bonds: A:S.12, A:K.38, A:D.40, A:Y.42, B:T.194, B:K.195, B:Q.198 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: 1 interactions with chain D, 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: D:Q.112, A:T.194, A:K.195, A:Q.198, B:S.12, B:K.38, B:D.40, B:Y.42 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 UTP.10: 16 residues within 4Å: Chain E: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain F: K.193, T.194, K.195, Q.198, F.233 Chain G: Q.112 Ligands: ATP.9 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:S.12, E:K.38, E:D.40, E:Y.42, F:T.194, F:K.195, F:Q.198 Salt bridges: F:K.193 UTP.12: 16 residues within 4Å: Chain E: K.193, T.194, K.195, Q.198, F.233 Chain F: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain H: Q.112 Ligands: ATP.11 9 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F, 1 interactions with chain H Hydrogen bonds: E:T.194, E:K.195, E:Q.198, F:S.12, F:K.38, F:D.40, F:Y.42, H:Q.112 Salt bridges: E:K.193 UTP.14: 16 residues within 4Å: Chain E: Q.112 Chain G: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain H: K.193, T.194, K.195, Q.198, F.233 Ligands: ATP.13 12 PLIP interactions: 7 interactions with chain G, 5 interactions with chain H Hydrogen bonds: G:S.12, G:K.38, G:D.40, G:D.40, G:Y.42, G:Y.42, G:E.146, H:T.194, H:T.194, H:K.195, H:Q.198 Salt bridges: H:K.193 UTP.16: 16 residues within 4Å: Chain F: Q.112 Chain G: K.193, T.194, K.195, Q.198, F.233 Chain H: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Ligands: ATP.15 13 PLIP interactions: 5 interactions with chain G, 7 interactions with chain H, 1 interactions with chain F Hydrogen bonds: G:T.194, G:T.194, G:K.195, G:Q.198, H:S.12, H:K.38, H:D.40, H:D.40, H:Y.42, H:Y.42, H:E.146, F:Q.112 Salt bridges: G:K.193 UTP.18: 16 residues within 4Å: Chain I: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain J: K.193, T.194, K.195, Q.198, F.233 Chain K: Q.112 Ligands: ATP.17 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:S.12, I:K.38, I:D.40, I:Y.42, J:T.194, J:K.195, J:Q.198 Salt bridges: J:K.193 UTP.20: 16 residues within 4Å: Chain I: K.193, T.194, K.195, Q.198, F.233 Chain J: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain L: Q.112 Ligands: ATP.19 9 PLIP interactions: 4 interactions with chain J, 4 interactions with chain I, 1 interactions with chain L Hydrogen bonds: J:S.12, J:K.38, J:D.40, J:Y.42, I:T.194, I:K.195, I:Q.198, L:Q.112 Salt bridges: I:K.193 UTP.22: 16 residues within 4Å: Chain I: Q.112 Chain K: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain L: K.193, T.194, K.195, Q.198, F.233 Ligands: ATP.21 12 PLIP interactions: 7 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:S.12, K:K.38, K:D.40, K:D.40, K:Y.42, K:Y.42, K:E.146, L:T.194, L:T.194, L:K.195, L:Q.198 Salt bridges: L:K.193 UTP.24: 16 residues within 4Å: Chain J: Q.112 Chain K: K.193, T.194, K.195, Q.198, F.233 Chain L: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Ligands: ATP.23 13 PLIP interactions: 1 interactions with chain J, 7 interactions with chain L, 5 interactions with chain K Hydrogen bonds: J:Q.112, L:S.12, L:K.38, L:D.40, L:D.40, L:Y.42, L:Y.42, L:E.146, K:T.194, K:T.194, K:K.195, K:Q.198 Salt bridges: K:K.193 UTP.26: 16 residues within 4Å: Chain M: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain N: K.193, T.194, K.195, Q.198, F.233 Chain O: Q.112 Ligands: ATP.25 8 PLIP interactions: 4 interactions with chain M, 4 interactions with chain N Hydrogen bonds: M:S.12, M:K.38, M:D.40, M:Y.42, N:T.194, N:K.195, N:Q.198 Salt bridges: N:K.193 UTP.28: 16 residues within 4Å: Chain M: K.193, T.194, K.195, Q.198, F.233 Chain N: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain P: Q.112 Ligands: ATP.27 9 PLIP interactions: 4 interactions with chain M, 4 interactions with chain N, 1 interactions with chain P Hydrogen bonds: M:T.194, M:K.195, M:Q.198, N:S.12, N:K.38, N:D.40, N:Y.42, P:Q.112 Salt bridges: M:K.193 UTP.30: 16 residues within 4Å: Chain M: Q.112 Chain O: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Chain P: K.193, T.194, K.195, Q.198, F.233 Ligands: ATP.29 12 PLIP interactions: 5 interactions with chain P, 7 interactions with chain O Hydrogen bonds: P:T.194, P:T.194, P:K.195, P:Q.198, O:S.12, O:K.38, O:D.40, O:D.40, O:Y.42, O:Y.42, O:E.146 Salt bridges: P:K.193 UTP.32: 16 residues within 4Å: Chain N: Q.112 Chain O: K.193, T.194, K.195, Q.198, F.233 Chain P: S.12, K.38, D.40, P.41, Y.42, E.146, G.148, G.149, E.155 Ligands: ATP.31 13 PLIP interactions: 7 interactions with chain P, 5 interactions with chain O, 1 interactions with chain N Hydrogen bonds: P:S.12, P:K.38, P:D.40, P:D.40, P:Y.42, P:Y.42, P:E.146, O:T.194, O:T.194, O:K.195, O:Q.198, N:Q.112 Salt bridges: O: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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

CTP synthase 1

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