SMTL ID : 6th2.2 (1 other biounit)

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

CTP.1: 16 residues within 4Å: Chain A: M.98, A.100, V.102, A.103, D.104, D.131, D.132, V.133, L.134, G.154, F.155, K.173, K.177 Chain B: K.116, K.117 Ligands: CA.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.102 Hydrogen bonds: A:M.98, A:D.131, A:D.132, A:V.133, A:L.134, A:F.155, B:K.117 Water bridges: A:D.132, A:K.177, A:K.177 Salt bridges: A:K.173, A:K.173, A:K.173, A:K.177, A:K.177 pi-Cation interactions: A:K.177 CTP.6: 16 residues within 4Å: Chain B: M.98, A.100, V.102, A.103, D.104, D.131, D.132, V.133, L.134, G.154, F.155, A.156, K.173, R.176, K.177 Ligands: CA.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.102 Hydrogen bonds: B:M.98, B:D.131, B:V.133, B:L.134, B:F.155, B:E.158 Salt bridges: B:K.173, B:K.173, B:R.176, B:R.176, B:K.177, B:K.177

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.104 Ligands: CTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.104, A:D.104, H2O.1, H2O.8 CA.7: 2 residues within 4Å: Chain B: D.104 Ligands: CTP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.104

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: T.22, I.32, G.33, N.34, A.103 Chain B: R.30 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Water bridges: B:K.114, B:K.114, A:D.104 Salt bridges: B:R.30, B:K.114 Hydrophobic interactions: A:I.32, A:A.103 Hydrogen bonds: A:N.34 ACT.4: 1 residues within 4Å: Chain A: R.176 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.175, A:E.175, A:E.175 Salt bridges: A:R.176 ACT.8: 6 residues within 4Å: Chain A: R.30 Chain B: T.22, I.32, G.33, N.34, A.103 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.103 Hydrogen bonds: B:N.34, B:D.104 Water bridges: A:R.30, A:R.30 Salt bridges: A:R.30

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 11 residues within 4Å: Chain A: S.36, S.37, G.38, K.39, Q.40, G.41, A.99, A.101, F.155, A.156, A.157 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.37, A:G.38, A:K.39, A:Q.40, A:G.41 Water bridges: A:G.20, A:K.217 Salt bridges: A:K.217 MES.9: 11 residues within 4Å: Chain B: S.36, S.37, G.38, K.39, Q.40, G.41, A.99, A.100, A.101, F.155, V.187 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.37, B:G.38, B:K.39, B:Q.40, B:G.41, B:A.157 Water bridges: B:G.20, B:S.36

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Coenzyme A biosynthesis bifunctional protein CoaBC

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