SMTL ID : 7zm1.1

Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC7b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x IY8: methoxy-[(~{E},3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]tridec-11-enyl]phosphinous acid(Covalent)

IY8.1: 18 residues within 4Å: Chain A: G.44, G.45, G.46, N.89, S.114, L.115, G.140, G.141, L.158, S.159, S.162, F.173, T.205, M.208, F.212, V.243, N.244, H.269 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.158, A:F.212 Hydrogen bonds: A:G.45, A:L.115, A:G.141 IY8.6: 18 residues within 4Å: Chain B: G.44, G.45, G.46, N.89, S.114, L.115, G.140, G.141, V.155, L.158, S.159, S.162, F.173, G.209, F.212, V.243, N.244, H.269 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.155, B:L.158 Hydrogen bonds: B:G.45, B:L.115, B:G.141 IY8.8: 18 residues within 4Å: Chain C: G.44, G.45, G.46, N.89, S.114, L.115, G.140, G.141, L.158, S.159, S.162, F.173, T.205, M.208, F.212, V.243, N.244, H.269 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.158, C:F.212 Hydrogen bonds: C:G.45, C:L.115, C:G.141 IY8.13: 18 residues within 4Å: Chain D: G.44, G.45, G.46, N.89, S.114, L.115, G.140, G.141, V.155, L.158, S.159, S.162, F.173, G.209, F.212, V.243, N.244, H.269 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.155, D:L.158 Hydrogen bonds: D:G.45, D:L.115, D:G.141

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

SO4.2: 5 residues within 4Å: Chain A: R.90, R.122, D.126, E.225, R.228 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.122, A:R.122 Salt bridges: A:R.90, A:R.122, A:R.228 SO4.3: 4 residues within 4Å: Chain A: R.157, R.175, K.181 Chain B: K.156 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.157, A:R.175, A:K.181, B:K.156 SO4.4: 3 residues within 4Å: Chain A: R.224 Chain D: R.224, R.228 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Water bridges: A:E.225, D:R.224 Salt bridges: A:R.224, D:R.224, D:R.228 SO4.5: 4 residues within 4Å: Chain A: P.232, R.258 Chain C: Q.266, K.275 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.133, C:Q.266 Water bridges: A:Q.260 Salt bridges: A:R.258, C:K.275 SO4.7: 5 residues within 4Å: Chain A: K.156 Chain B: R.157, R.175, V.176, K.181 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.157, B:R.175, B:K.181, A:K.156 SO4.9: 5 residues within 4Å: Chain C: R.90, R.122, D.126, E.225, R.228 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.122, C:R.122 Salt bridges: C:R.90, C:R.122, C:R.228 SO4.10: 4 residues within 4Å: Chain C: R.157, R.175, K.181 Chain D: K.156 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:K.156, C:R.157, C:R.175, C:K.181 SO4.11: 3 residues within 4Å: Chain B: R.224, R.228 Chain C: R.224 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:E.225, B:R.224 Salt bridges: C:R.224, B:R.224, B:R.228 SO4.12: 4 residues within 4Å: Chain A: Q.266, K.275 Chain C: P.232, R.258 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.266, C:R.133 Water bridges: A:E.278, A:E.278 Salt bridges: A:K.275, C:R.258 SO4.14: 5 residues within 4Å: Chain C: K.156 Chain D: R.157, R.175, V.176, K.181 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.157, D:R.175, D:K.181, C:K.156

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
B

C
A

D
B

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

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