SMTL ID : 6tgv.1

Crystal structure of Mycobacterium smegmatis CoaBC in complex with CTP and FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

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

CTP.1: 14 residues within 4Å: Chain A: M.276, A.278, V.280, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335, K.351 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.280 Hydrogen bonds: A:M.276, A:D.309, A:V.311, A:L.312, A:F.333, A:A.335 Salt bridges: A:K.351 CTP.7: 12 residues within 4Å: Chain B: M.276, A.278, V.280, A.281, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.280 Hydrogen bonds: B:M.276, B:A.281, B:V.311, B:L.312, B:F.333, B:A.335 CTP.11: 12 residues within 4Å: Chain C: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, F.333, A.334, A.335 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.280 Hydrogen bonds: C:M.276, C:D.282, C:D.309, C:D.310, C:V.311, C:L.312, C:F.333, C:A.335 CTP.14: 12 residues within 4Å: Chain D: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.280 Hydrogen bonds: D:M.276, D:D.309, D:D.310, D:V.311, D:L.312, D:F.333 CTP.17: 14 residues within 4Å: Chain E: M.276, A.278, V.280, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335, K.351 Ligands: MG.21 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.280 Hydrogen bonds: E:M.276, E:D.309, E:V.311, E:L.312, E:F.333, E:A.335 Salt bridges: E:K.351 CTP.23: 12 residues within 4Å: Chain F: M.276, A.278, V.280, A.281, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:V.280 Hydrogen bonds: F:M.276, F:A.281, F:V.311, F:L.312, F:F.333, F:A.335 CTP.27: 12 residues within 4Å: Chain G: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, F.333, A.334, A.335 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.280 Hydrogen bonds: G:M.276, G:D.282, G:D.309, G:D.310, G:V.311, G:L.312, G:F.333, G:A.335 CTP.30: 12 residues within 4Å: Chain H: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:V.280 Hydrogen bonds: H:M.276, H:D.309, H:D.310, H:V.311, H:L.312, H:F.333 CTP.33: 14 residues within 4Å: Chain I: M.276, A.278, V.280, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335, K.351 Ligands: MG.37 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:V.280 Hydrogen bonds: I:M.276, I:D.309, I:V.311, I:L.312, I:F.333, I:A.335 Salt bridges: I:K.351 CTP.39: 12 residues within 4Å: Chain J: M.276, A.278, V.280, A.281, D.309, D.310, V.311, L.312, G.332, F.333, A.334, A.335 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:V.280 Hydrogen bonds: J:M.276, J:A.281, J:V.311, J:L.312, J:F.333, J:A.335 CTP.43: 12 residues within 4Å: Chain K: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, F.333, A.334, A.335 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.280 Hydrogen bonds: K:M.276, K:D.282, K:D.309, K:D.310, K:V.311, K:L.312, K:F.333, K:A.335 CTP.46: 12 residues within 4Å: Chain L: M.276, A.278, V.280, A.281, D.282, D.309, D.310, V.311, L.312, G.332, F.333, A.334 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:V.280 Hydrogen bonds: L:M.276, L:D.309, L:D.310, L:V.311, L:L.312, L:F.333

21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: L.44, G.48, A.49 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: A.17, K.20, A.121, M.122, R.163, L.164 Ligands: FMN.6 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: R.7, I.8, S.34, R.36, I.76 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: A.17, K.20, G.162, R.163, L.164 Ligands: FMN.10 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain C: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain D: E.148, Y.186, A.227, G.230, A.231 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain E: L.44, G.48, A.49 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain E: A.17, K.20, A.121, M.122, R.163, L.164 Ligands: FMN.22 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain E: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain F: R.7, I.8, S.34, R.36, I.76 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain F: A.17, K.20, G.162, R.163, L.164 Ligands: FMN.26 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain G: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain H: E.148, Y.186, A.227, G.230, A.231 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain I: L.44, G.48, A.49 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain I: A.17, K.20, A.121, M.122, R.163, L.164 Ligands: FMN.38 Ligand excluded by PLIP EDO.36: 8 residues within 4Å: Chain I: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain J: R.7, I.8, S.34, R.36, I.76 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain J: A.17, K.20, G.162, R.163, L.164 Ligands: FMN.42 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain K: G.143, V.145, L.177, A.181, D.182, A.183, L.184, P.185 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain L: E.148, Y.186, A.227, G.230, A.231 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.282 Ligands: CTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.282 MG.21: 2 residues within 4Å: Chain E: D.282 Ligands: CTP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.282 MG.37: 2 residues within 4Å: Chain I: D.282 Ligands: CTP.33 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.282

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 23 residues within 4Å: Chain A: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain B: A.54 Chain E: V.64, F.65, V.68, H.73, A.101, D.102 Ligands: EDO.3 17 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E, 13 interactions with chain A Hydrophobic interactions: B:A.54, E:F.65, E:V.68, A:I.16, A:F.46 pi-Stacking: E:H.73, A:F.46 Hydrogen bonds: A:G.14, A:I.16, A:S.42, A:S.42, A:T.89, A:T.89, A:A.90, A:R.95, A:A.121 Water bridges: A:E.41 FMN.10: 21 residues within 4Å: Chain A: A.54 Chain B: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain D: V.64, F.65, A.101, D.102 Ligands: EDO.9 17 PLIP interactions: 14 interactions with chain B, 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:I.16, B:F.46, D:F.65, A:A.54 Hydrogen bonds: B:G.14, B:I.16, B:T.40, B:S.42, B:S.42, B:T.89, B:A.90, B:D.91, B:L.92, B:A.121, D:A.101 Salt bridges: B:R.95 pi-Stacking: B:F.46 FMN.13: 21 residues within 4Å: Chain C: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 Chain D: A.54 Chain J: V.64, F.65, V.68, H.73, A.101, D.102 17 PLIP interactions: 1 interactions with chain D, 3 interactions with chain J, 13 interactions with chain C Hydrophobic interactions: D:A.54, J:F.65, J:V.68, C:I.16, C:F.46 pi-Stacking: J:H.73, C:F.46 Hydrogen bonds: C:G.14, C:I.16, C:T.40, C:S.42, C:S.42, C:A.90, C:D.91, C:A.121 Water bridges: C:S.42 Salt bridges: C:R.95 FMN.16: 20 residues within 4Å: Chain C: A.54 Chain D: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 Chain G: V.64, F.65, V.68, H.73, A.101 19 PLIP interactions: 14 interactions with chain D, 4 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: D:I.16, D:F.46, G:F.65, G:V.68, C:A.54 Hydrogen bonds: D:G.14, D:I.16, D:T.40, D:S.42, D:S.42, D:T.89, D:A.90, D:D.91, D:R.95, D:A.121, G:A.101 Water bridges: D:T.89 pi-Stacking: D:F.46, G:H.73 FMN.22: 23 residues within 4Å: Chain E: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain F: A.54 Chain I: V.64, F.65, V.68, H.73, A.101, D.102 Ligands: EDO.19 17 PLIP interactions: 3 interactions with chain I, 13 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: I:F.65, I:V.68, E:I.16, E:F.46, F:A.54 pi-Stacking: I:H.73, E:F.46 Hydrogen bonds: E:G.14, E:I.16, E:S.42, E:S.42, E:T.89, E:T.89, E:A.90, E:R.95, E:A.121 Water bridges: E:E.41 FMN.26: 21 residues within 4Å: Chain E: A.54 Chain F: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain H: V.64, F.65, A.101, D.102 Ligands: EDO.25 17 PLIP interactions: 2 interactions with chain H, 14 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: H:F.65, F:I.16, F:F.46, E:A.54 Hydrogen bonds: H:A.101, F:G.14, F:I.16, F:T.40, F:S.42, F:S.42, F:T.89, F:A.90, F:D.91, F:L.92, F:A.121 Salt bridges: F:R.95 pi-Stacking: F:F.46 FMN.29: 21 residues within 4Å: Chain B: V.64, F.65, V.68, H.73, A.101, D.102 Chain G: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 Chain H: A.54 17 PLIP interactions: 13 interactions with chain G, 3 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: G:I.16, G:F.46, B:F.65, B:V.68, H:A.54 Hydrogen bonds: G:G.14, G:I.16, G:T.40, G:S.42, G:S.42, G:A.90, G:D.91, G:A.121 Water bridges: G:S.42 Salt bridges: G:R.95 pi-Stacking: G:F.46, B:H.73 FMN.32: 20 residues within 4Å: Chain G: A.54 Chain H: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 Chain K: V.64, F.65, V.68, H.73, A.101 19 PLIP interactions: 14 interactions with chain H, 1 interactions with chain G, 4 interactions with chain K Hydrophobic interactions: H:I.16, H:F.46, G:A.54, K:F.65, K:V.68 Hydrogen bonds: H:G.14, H:I.16, H:T.40, H:S.42, H:S.42, H:T.89, H:A.90, H:D.91, H:R.95, H:A.121, K:A.101 Water bridges: H:T.89 pi-Stacking: H:F.46, K:H.73 FMN.38: 23 residues within 4Å: Chain A: V.64, F.65, V.68, H.73, A.101, D.102 Chain I: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain J: A.54 Ligands: EDO.35 17 PLIP interactions: 13 interactions with chain I, 3 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: I:I.16, I:F.46, A:F.65, A:V.68, J:A.54 Hydrogen bonds: I:G.14, I:I.16, I:S.42, I:S.42, I:T.89, I:T.89, I:A.90, I:R.95, I:A.121 Water bridges: I:E.41 pi-Stacking: I:F.46, A:H.73 FMN.42: 21 residues within 4Å: Chain I: A.54 Chain J: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122, M.126 Chain L: V.64, F.65, A.101, D.102 Ligands: EDO.41 17 PLIP interactions: 14 interactions with chain J, 2 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: J:I.16, J:F.46, L:F.65, I:A.54 Hydrogen bonds: J:G.14, J:I.16, J:T.40, J:S.42, J:S.42, J:T.89, J:A.90, J:D.91, J:L.92, J:A.121, L:A.101 Salt bridges: J:R.95 pi-Stacking: J:F.46 FMN.45: 21 residues within 4Å: Chain F: V.64, F.65, V.68, H.73, A.101, D.102 Chain K: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 Chain L: A.54 17 PLIP interactions: 3 interactions with chain F, 13 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: F:F.65, F:V.68, K:I.16, K:F.46, L:A.54 pi-Stacking: F:H.73, K:F.46 Hydrogen bonds: K:G.14, K:I.16, K:T.40, K:S.42, K:S.42, K:A.90, K:D.91, K:A.121 Water bridges: K:S.42 Salt bridges: K:R.95 FMN.48: 20 residues within 4Å: Chain C: V.64, F.65, V.68, H.73, A.101 Chain K: A.54 Chain L: A.13, G.14, G.15, I.16, T.40, S.42, F.46, T.89, A.90, D.91, L.92, R.95, A.121, M.122 19 PLIP interactions: 14 interactions with chain L, 4 interactions with chain C, 1 interactions with chain K Hydrophobic interactions: L:I.16, L:F.46, C:F.65, C:V.68, K:A.54 Hydrogen bonds: L:G.14, L:I.16, L:T.40, L:S.42, L:S.42, L:T.89, L:A.90, L:D.91, L:R.95, L:A.121, C:A.101 Water bridges: L:T.89 pi-Stacking: L:F.46, C:H.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mendes, V. et al., Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site. Nat Commun (2021)

Release Date

2020-11-25

Peptides

Coenzyme A biosynthesis bifunctional protein CoaBC: ABCDEFGHIJKL

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

Coenzyme A biosynthesis bifunctional protein CoaBC