SMTL ID : 7qwn.1 (2 other biounits)

Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-trimer

Ligands

3 x DQE: ethyl 5-pyridin-4-yl-1~{H}-indole-2-carboxylate(Non-covalent)

DQE.1: 17 residues within 4Å: Chain A: F.85, I.89, D.93, V.96, Q.97, M.185, N.188, P.198, K.199, S.202, A.203, I.206, F.245 Chain B: L.278, V.282, P.284, L.345 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.93, A:V.96, A:I.206 Hydrogen bonds: A:K.199 Water bridges: A:N.188 Salt bridges: A:K.199 DQE.12: 12 residues within 4Å: Chain B: I.82, F.85, Q.97, L.102, V.252, A.253, E.256, T.257, F.301, W.399, L.400 Ligands: HEM.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.82, B:Q.97, B:V.252, B:A.253, B:T.257, B:F.301, B:L.400 pi-Stacking: B:W.399, B:W.399 DQE.18: 11 residues within 4Å: Chain C: I.82, L.102, M.185, V.252, A.253, E.256, T.257, F.301, W.399, L.400 Ligands: HEM.19 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.82, C:V.252, C:A.253, C:T.257, C:F.301 Water bridges: C:M.185 pi-Stacking: C:W.399, C:W.399

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 34 residues within 4Å: Chain A: S.68, M.101, L.102, H.109, R.113, F.120, I.164, L.167, M.249, L.250, A.253, G.254, T.257, T.258, S.261, V.292, P.297, V.298, F.301, R.303, Y.326, G.353, F.354, G.355, G.356, A.359, H.360, Y.361, C.362, I.363, G.364, L.367, A.368, I.372 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.102, A:F.120, A:L.250, A:A.253, A:P.297, A:F.301, A:Y.326, A:F.354, A:I.363, A:I.363, A:L.367, A:A.368 Hydrogen bonds: A:G.356, A:G.356 Water bridges: A:R.303, A:H.360 Salt bridges: A:H.109, A:R.113, A:R.303, A:H.360 pi-Stacking: A:F.354 Metal complexes: A:C.362, H2O.3 HEM.13: 34 residues within 4Å: Chain B: M.101, L.102, H.109, R.113, F.120, I.164, L.167, M.249, L.250, A.253, G.254, T.257, T.258, S.261, V.292, P.297, V.298, F.301, R.303, Y.326, G.353, F.354, G.355, G.356, A.359, H.360, Y.361, C.362, I.363, G.364, L.367, A.368, I.372 Ligands: DQE.12 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:L.102, B:F.120, B:A.253, B:P.297, B:F.301, B:Y.326, B:F.354, B:I.363, B:L.367 Hydrogen bonds: B:Y.326 Water bridges: B:G.356, B:H.360 Salt bridges: B:H.109, B:R.113, B:R.303, B:H.360 pi-Stacking: B:F.354 Metal complexes: B:C.362 HEM.19: 34 residues within 4Å: Chain C: V.81, M.101, L.102, H.109, R.113, F.120, I.164, L.167, M.249, L.250, A.253, G.254, T.257, T.258, S.261, V.292, P.297, V.298, F.301, R.303, Y.326, G.353, F.354, G.355, A.359, H.360, Y.361, C.362, I.363, G.364, L.367, A.368, I.372 Ligands: DQE.18 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.120, C:L.250, C:A.253, C:P.297, C:F.301, C:F.301, C:Y.326, C:F.354, C:I.363, C:I.363, C:L.367 Hydrogen bonds: C:Y.326 Salt bridges: C:H.109, C:R.113, C:R.303, C:H.360 pi-Stacking: C:F.354 Metal complexes: C:C.362

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

SO4.3: 3 residues within 4Å: Chain A: S.4, P.5, W.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.4, A:W.38 SO4.4: 2 residues within 4Å: Chain A: A.17, R.396 5 PLIP interactions: 5 interactions with chain A Water bridges: A:A.17, A:R.396, A:R.396, A:R.396 Salt bridges: A:R.396 SO4.5: 4 residues within 4Å: Chain A: R.135, K.138, Q.162, Q.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.172 Salt bridges: A:R.135 SO4.6: 3 residues within 4Å: Chain A: E.66, R.69, H.70 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.66 Salt bridges: A:R.69, A:H.70 SO4.7: 3 residues within 4Å: Chain A: R.113, S.117, I.363 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.117, A:S.117 Water bridges: A:R.113 Salt bridges: A:R.113 SO4.8: 4 residues within 4Å: Chain A: R.69, H.70, S.71, D.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.71, A:S.71, A:D.72, A:D.72 SO4.9: 4 residues within 4Å: Chain A: H.272, P.273, D.274, Q.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.272, A:D.274, A:Q.275 Water bridges: A:Q.275, A:Q.275 Salt bridges: A:H.272 SO4.14: 5 residues within 4Å: Chain B: P.16, R.84, K.86, N.87, R.396 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.87 Water bridges: B:R.84, B:R.84, B:N.87, B:N.87, B:D.88, B:R.396, B:R.396, B:R.396, B:R.396 Salt bridges: B:R.396 SO4.15: 2 residues within 4Å: Chain B: A.17, R.396 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.396 SO4.16: 8 residues within 4Å: Chain B: V.335, F.336, Q.337, R.346, N.347, P.348, N.349, P.350 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.335, B:Q.337 Water bridges: B:N.347, B:N.347 Salt bridges: B:R.346 SO4.17: 3 residues within 4Å: Chain B: P.44, G.45, H.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.45 Salt bridges: B:H.51 SO4.20: 5 residues within 4Å: Chain C: P.16, K.86, N.87, E.189, R.396 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.87, C:N.87 Water bridges: C:R.84, C:R.84, C:D.88, C:R.396 Salt bridges: C:R.396 SO4.21: 2 residues within 4Å: Chain C: A.17, R.396 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.396 SO4.22: 4 residues within 4Å: Chain C: H.272, P.273, D.274, Q.275 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.274, C:D.274, C:Q.275, C:Q.275 Water bridges: C:F.342 SO4.23: 3 residues within 4Å: Chain C: P.44, G.45, H.51 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.45 Water bridges: C:H.51 Salt bridges: C:H.51

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain A: F.336, Q.337, R.346 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.91, E.95, R.98 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: A.90, R.91, E.92 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: F.336, R.346, P.348, P.350 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katariya, M.M. et al., Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis. Chemistry (2023)

Release Date

2023-02-01

Peptides

Steroid C26-monooxygenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Steroid C26-monooxygenase

Related Entries With Identical Sequence