SMTL ID : 7zm2.1

Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC8b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x 9SW: methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid(Covalent)

9SW.1: 8 residues within 4Å: Chain A: G.45, G.46, S.114, L.115, F.173, V.243, H.269 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.45, A:L.115 9SW.5: 8 residues within 4Å: Chain B: G.45, G.46, S.114, L.115, F.173, V.243, H.269 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.45, B:L.115 9SW.9: 9 residues within 4Å: Chain C: G.44, G.45, G.46, S.114, L.115, F.173, V.243, H.269 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.45, C:L.115 9SW.12: 9 residues within 4Å: Chain D: G.44, G.45, G.46, S.114, L.115, F.173, V.243, H.269 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.45, D:L.115

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.157, R.175, V.176, K.181 Chain C: K.156 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Water bridges: A:K.181 Salt bridges: A:R.157, A:R.175, A:K.181, C:K.156 SO4.3: 5 residues within 4Å: Chain A: K.156 Chain C: R.157, R.175, V.176, K.181 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.157, C:R.175, C:K.181, A:K.156 SO4.4: 10 residues within 4Å: Chain A: G.44, G.45, G.46, A.49, N.54, N.113, F.173, R.192, W.270 Ligands: 9SW.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.45, A:G.46, A:N.54, A:N.113 Salt bridges: A:R.192 SO4.6: 5 residues within 4Å: Chain B: R.157, R.175, V.176, K.181 Chain D: K.156 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Water bridges: B:K.181 Salt bridges: B:R.157, B:R.175, B:K.181, D:K.156 SO4.7: 5 residues within 4Å: Chain B: K.156 Chain D: R.157, R.175, V.176, K.181 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.157, D:R.175, D:K.181, B:K.156 SO4.8: 10 residues within 4Å: Chain B: G.44, G.45, G.46, A.49, N.54, N.113, F.173, R.192, W.270 Ligands: 9SW.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.45, B:G.46, B:N.54, B:N.113 Salt bridges: B:R.192 SO4.10: 11 residues within 4Å: Chain C: G.44, G.45, G.46, A.49, N.54, N.113, F.173, R.192, H.269, W.270 Ligands: 9SW.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.46, C:N.54, C:N.113, C:W.270 Salt bridges: C:R.192 SO4.11: 3 residues within 4Å: Chain C: R.133, P.232, R.258 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.107, C:R.133, C:R.258 SO4.13: 11 residues within 4Å: Chain D: G.44, G.45, G.46, A.49, N.54, N.113, F.173, R.192, H.269, W.270 Ligands: 9SW.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.46, D:N.54, D:N.113, D:W.270 Salt bridges: D:R.192 SO4.14: 3 residues within 4Å: Chain D: R.133, P.232, R.258 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.107, D:R.133, D:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barelier, S. et al., Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis. Febs J. (2023)

Release Date

2022-09-28

Peptides

4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase

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