SMTL ID : 8uv4.1

M. tuberculosis CTP synthase filament bound to substrates

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 22 residues within 4Å: Chain A: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain C: P.194, S.195 Ligands: 5ZL.2, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.21, A:L.22, A:G.23, A:K.24, A:G.25, A:L.26, A:A.253, A:D.315 Salt bridges: A:K.24, A:H.81 ADP.6: 22 residues within 4Å: Chain B: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain D: P.194, S.195 Ligands: 5ZL.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.21, B:L.22, B:G.23, B:K.24, B:G.25, B:L.26, B:A.253, B:D.315 Salt bridges: B:K.24, B:H.81 ADP.11: 22 residues within 4Å: Chain A: P.194, S.195 Chain C: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.12, MG.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.21, C:G.23, C:K.24, C:G.25, C:L.26, C:D.78, C:H.81, C:A.253 Salt bridges: C:K.24 ADP.14: 22 residues within 4Å: Chain B: P.194, S.195 Chain D: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.15, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.21, D:G.23, D:K.24, D:G.25, D:L.26, D:D.78, D:H.81, D:A.253 Salt bridges: D:K.24 ADP.17: 22 residues within 4Å: Chain E: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain G: P.194, S.195 Ligands: 5ZL.18, MG.19 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.21, E:G.23, E:K.24, E:G.25, E:L.26, E:D.78, E:H.81, E:A.253, E:D.315 Salt bridges: E:K.24 ADP.21: 22 residues within 4Å: Chain F: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain H: P.194, S.195 Ligands: 5ZL.22, MG.23 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.21, F:G.23, F:K.24, F:G.25, F:L.26, F:D.78, F:H.81, F:A.253, F:D.315 Salt bridges: F:K.24 ADP.25: 22 residues within 4Å: Chain E: P.194, S.195 Chain G: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.26, MG.27 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:S.21, G:L.22, G:G.23, G:K.24, G:G.25, G:L.26, G:A.253 Salt bridges: G:K.24, G:H.81 ADP.29: 22 residues within 4Å: Chain F: P.194, S.195 Chain H: S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.30, MG.31 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:S.21, H:L.22, H:G.23, H:K.24, H:G.25, H:L.26, H:A.253 Salt bridges: H:K.24, H:H.81 ADP.33: 23 residues within 4Å: Chain I: S.20, S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain K: P.194, S.195 Ligands: 5ZL.34, MG.35 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:S.21, I:G.23, I:K.24, I:G.25, I:L.26, I:D.78, I:H.81, I:A.253, I:D.315 Salt bridges: I:K.24 ADP.37: 23 residues within 4Å: Chain J: S.20, S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Chain L: P.194, S.195 Ligands: 5ZL.38, MG.39 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.21, J:G.23, J:K.24, J:G.25, J:L.26, J:D.78, J:H.81, J:A.253, J:D.315 Salt bridges: J:K.24 ADP.42: 23 residues within 4Å: Chain I: P.194, S.195 Chain K: S.20, S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.43, MG.44 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:S.21, K:G.23, K:K.24, K:G.25, K:L.26, K:D.78, K:H.81, K:A.253 Salt bridges: K:K.24 ADP.46: 23 residues within 4Å: Chain J: P.194, S.195 Chain L: S.20, S.21, L.22, G.23, K.24, G.25, L.26, D.78, H.81, E.152, R.223, T.250, P.251, D.252, A.253, I.256, I.259, D.315, L.318 Ligands: 5ZL.47, MG.48 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:S.21, L:G.23, L:K.24, L:G.25, L:L.26, L:D.78, L:H.81, L:A.253 Salt bridges: L:K.24

12 x 5ZL: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

5ZL.2: 25 residues within 4Å: Chain A: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain C: K.199, T.200, K.201, Q.204, K.235 Chain D: T.118, Q.120 Ligands: ADP.1, MG.3, MG.4 24 PLIP interactions: 13 interactions with chain A, 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:S.20, A:K.46, A:Y.50, A:H.63, A:D.78, A:G.155, A:D.159, A:D.159, A:E.161, A:E.161, C:T.200, C:T.200, C:T.200, C:K.201, C:Q.204, D:Q.120 Salt bridges: A:K.24, A:K.46, C:K.199, C:K.201, C:K.201, C:K.235, C:K.235 pi-Cation interactions: A:H.63 5ZL.7: 25 residues within 4Å: Chain B: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain C: T.118, Q.120 Chain D: K.199, T.200, K.201, Q.204, K.235 Ligands: ADP.6, MG.8, MG.9 24 PLIP interactions: 13 interactions with chain B, 10 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:S.20, B:K.46, B:Y.50, B:H.63, B:D.78, B:G.155, B:D.159, B:D.159, B:E.161, B:E.161, D:T.200, D:T.200, D:T.200, D:K.201, D:Q.204, C:Q.120 Salt bridges: B:K.24, B:K.46, D:K.199, D:K.201, D:K.201, D:K.235, D:K.235 pi-Cation interactions: B:H.63 5ZL.12: 25 residues within 4Å: Chain A: K.199, T.200, K.201, Q.204, K.235 Chain B: T.118, Q.120 Chain C: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: MG.5, ADP.11, MG.13 23 PLIP interactions: 1 interactions with chain B, 12 interactions with chain C, 10 interactions with chain A Hydrogen bonds: B:Q.120, C:S.20, C:K.46, C:D.48, C:Y.50, C:H.63, C:D.78, C:G.155, C:D.159, C:E.161, A:T.200, A:T.200, A:T.200, A:K.201, A:Q.204 Salt bridges: C:K.24, C:K.46, A:K.199, A:K.201, A:K.201, A:K.235, A:K.235 pi-Cation interactions: C:H.63 5ZL.15: 25 residues within 4Å: Chain A: T.118, Q.120 Chain B: K.199, T.200, K.201, Q.204, K.235 Chain D: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: MG.10, ADP.14, MG.16 24 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: D:S.20, D:K.46, D:D.48, D:Y.50, D:H.63, D:D.78, D:G.155, D:D.159, D:E.161, A:Q.120, B:T.200, B:T.200, B:T.200, B:K.201, B:Q.204 Salt bridges: D:K.24, D:K.46, B:K.199, B:K.199, B:K.201, B:K.201, B:K.235, B:K.235 pi-Cation interactions: D:H.63 5ZL.18: 25 residues within 4Å: Chain E: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain G: K.199, T.200, K.201, Q.204, K.235 Chain H: T.118, Q.120 Ligands: ADP.17, MG.19, MG.20 25 PLIP interactions: 13 interactions with chain E, 11 interactions with chain G, 1 interactions with chain H Hydrogen bonds: E:S.20, E:K.46, E:Y.50, E:H.63, E:D.78, E:G.155, E:D.159, E:D.159, E:E.161, E:E.161, G:T.200, G:T.200, G:T.200, G:K.201, G:Q.204, H:Q.120 Salt bridges: E:K.24, E:K.46, G:K.199, G:K.199, G:K.201, G:K.201, G:K.235, G:K.235 pi-Cation interactions: E:H.63 5ZL.22: 25 residues within 4Å: Chain F: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain G: T.118, Q.120 Chain H: K.199, T.200, K.201, Q.204, K.235 Ligands: ADP.21, MG.23, MG.24 25 PLIP interactions: 11 interactions with chain H, 1 interactions with chain G, 13 interactions with chain F Hydrogen bonds: H:T.200, H:T.200, H:T.200, H:K.201, H:Q.204, G:Q.120, F:S.20, F:K.46, F:Y.50, F:H.63, F:D.78, F:G.155, F:D.159, F:D.159, F:E.161, F:E.161 Salt bridges: H:K.199, H:K.199, H:K.201, H:K.201, H:K.235, H:K.235, F:K.24, F:K.46 pi-Cation interactions: F:H.63 5ZL.26: 25 residues within 4Å: Chain E: K.199, T.200, K.201, Q.204, K.235 Chain F: T.118, Q.120 Chain G: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: ADP.25, MG.27, MG.28 23 PLIP interactions: 12 interactions with chain G, 1 interactions with chain F, 10 interactions with chain E Hydrogen bonds: G:S.20, G:K.46, G:D.48, G:Y.50, G:H.63, G:D.78, G:G.155, G:D.159, G:E.161, F:Q.120, E:T.200, E:T.200, E:T.200, E:K.201, E:Q.204 Salt bridges: G:K.24, G:K.46, E:K.199, E:K.201, E:K.201, E:K.235, E:K.235 pi-Cation interactions: G:H.63 5ZL.30: 25 residues within 4Å: Chain E: T.118, Q.120 Chain F: K.199, T.200, K.201, Q.204, K.235 Chain H: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: ADP.29, MG.31, MG.32 23 PLIP interactions: 12 interactions with chain H, 10 interactions with chain F, 1 interactions with chain E Hydrogen bonds: H:S.20, H:K.46, H:D.48, H:Y.50, H:H.63, H:D.78, H:G.155, H:D.159, H:E.161, F:T.200, F:T.200, F:T.200, F:K.201, F:Q.204, E:Q.120 Salt bridges: H:K.24, H:K.46, F:K.199, F:K.201, F:K.201, F:K.235, F:K.235 pi-Cation interactions: H:H.63 5ZL.34: 25 residues within 4Å: Chain I: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain K: K.199, T.200, K.201, Q.204, K.235 Chain L: T.118, Q.120 Ligands: ADP.33, MG.35, MG.41 22 PLIP interactions: 11 interactions with chain I, 10 interactions with chain K, 1 interactions with chain L Hydrogen bonds: I:S.20, I:K.46, I:Y.50, I:G.155, I:D.159, I:D.159, I:E.161, I:E.161, K:T.200, K:T.200, K:T.200, K:K.201, K:Q.204, L:Q.120 Salt bridges: I:K.24, I:K.46, K:K.199, K:K.201, K:K.201, K:K.235, K:K.235 pi-Cation interactions: I:H.63 5ZL.38: 25 residues within 4Å: Chain J: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Chain K: T.118, Q.120 Chain L: K.199, T.200, K.201, Q.204, K.235 Ligands: ADP.37, MG.39, MG.45 22 PLIP interactions: 1 interactions with chain K, 11 interactions with chain J, 10 interactions with chain L Hydrogen bonds: K:Q.120, J:S.20, J:K.46, J:Y.50, J:G.155, J:D.159, J:D.159, J:E.161, J:E.161, L:T.200, L:T.200, L:T.200, L:K.201, L:Q.204 Salt bridges: J:K.24, J:K.46, L:K.199, L:K.201, L:K.201, L:K.235, L:K.235 pi-Cation interactions: J:H.63 5ZL.43: 25 residues within 4Å: Chain I: K.199, T.200, K.201, Q.204, K.235 Chain J: T.118, Q.120 Chain K: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: MG.36, ADP.42, MG.44 21 PLIP interactions: 10 interactions with chain I, 10 interactions with chain K, 1 interactions with chain J Hydrogen bonds: I:T.200, I:T.200, I:T.200, I:K.201, I:Q.204, K:S.20, K:K.46, K:D.48, K:Y.50, K:G.155, K:D.159, K:E.161, J:Q.120 Salt bridges: I:K.199, I:K.201, I:K.201, I:K.235, I:K.235, K:K.24, K:K.46 pi-Cation interactions: K:H.63 5ZL.47: 25 residues within 4Å: Chain I: T.118, Q.120 Chain J: K.199, T.200, K.201, Q.204, K.235 Chain L: S.20, S.21, K.24, K.46, D.48, P.49, Y.50, H.63, D.78, E.152, G.154, G.155, T.156, D.159, E.161 Ligands: MG.40, ADP.46, MG.48 21 PLIP interactions: 10 interactions with chain J, 10 interactions with chain L, 1 interactions with chain I Hydrogen bonds: J:T.200, J:T.200, J:T.200, J:K.201, J:Q.204, L:S.20, L:K.46, L:D.48, L:Y.50, L:G.155, L:D.159, L:E.161, I:Q.120 Salt bridges: J:K.199, J:K.201, J:K.201, J:K.235, J:K.235, L:K.24, L:K.46 pi-Cation interactions: L:H.63

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

MG.3: 3 residues within 4Å: Chain A: S.21 Ligands: ADP.1, 5ZL.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain C: K.199, K.235 Ligands: 5ZL.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: K.199 Ligands: 5ZL.12 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: S.21 Ligands: ADP.6, 5ZL.7 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain D: K.199, K.235 Ligands: 5ZL.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: K.199 Ligands: 5ZL.15 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: S.21 Ligands: ADP.11, 5ZL.12 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: S.21 Ligands: ADP.14, 5ZL.15 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain E: S.21 Ligands: ADP.17, 5ZL.18 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain G: K.199 Ligands: 5ZL.18 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain F: S.21 Ligands: ADP.21, 5ZL.22 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain H: K.199 Ligands: 5ZL.22 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain G: S.21 Ligands: ADP.25, 5ZL.26 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain E: K.199, K.235 Ligands: 5ZL.26 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain H: S.21 Ligands: ADP.29, 5ZL.30 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain F: K.199, K.235 Ligands: 5ZL.30 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Ligands: ADP.33, 5ZL.34 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain I: K.199, K.235 Ligands: 5ZL.43 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Ligands: ADP.37, 5ZL.38 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain J: K.199, K.235 Ligands: 5ZL.47 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain K: K.199, K.235 Ligands: 5ZL.34 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Ligands: ADP.42, 5ZL.43 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain L: K.199, K.235 Ligands: 5ZL.38 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Ligands: ADP.46, 5ZL.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., M. tuberculosis CTP synthase filament bound to substrates. To Be Published

Release Date

2025-07-02

Peptides

CTP synthase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
V

C
X

D
b

E
A

F
E

G
G

H
K

I
B

J
F

K
H

L
L

CTP synthase

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