SMTL ID : 3zby.1 (3 other biounits)

Ligand-free structure of CYP142 from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC- GLC- GLC- GLC- GLC- GLC: Cycloheptakis-(1-4)-(alpha-D-glucopyranose)(Non-covalent)

GLC-GLC-GLC-GLC-GLC-GLC-GLC.1: 6 residues within 4Å: Chain A: P.76, M.179, F.182, K.190, D.221, F.225 No protein-ligand interaction detected (PLIP) GLC-GLC-GLC-GLC-GLC-GLC-GLC.2: 4 residues within 4Å: Chain B: M.179, K.190, D.221, F.225 No protein-ligand interaction detected (PLIP)

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

HEM.3: 30 residues within 4Å: Chain A: E.56, M.78, I.79, H.86, R.90, F.97, I.230, G.233, G.234, T.237, T.238, T.241, L.274, P.279, V.280, M.283, R.285, F.308, A.335, F.336, G.337, F.338, T.340, H.341, C.343, L.344, G.345, L.348, A.349 Ligands: EDO.7 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.97, A:I.230, A:T.237, A:L.274, A:P.279, A:V.280, A:V.280, A:F.308, A:F.336, A:F.336, A:L.344, A:L.348, A:A.349 Hydrogen bonds: A:F.338, A:F.338 Water bridges: A:H.341 Salt bridges: A:H.86, A:R.90, A:R.285, A:H.341 pi-Stacking: A:F.336 Metal complexes: A:C.343 HEM.8: 29 residues within 4Å: Chain B: E.56, M.78, I.79, H.86, R.90, F.97, I.230, G.233, G.234, T.237, T.238, T.241, L.274, P.279, V.280, M.283, R.285, F.308, A.335, F.336, G.337, F.338, T.340, H.341, C.343, L.344, G.345, A.349 Ligands: EDO.12 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:I.79, B:F.97, B:I.230, B:L.274, B:P.279, B:V.280, B:V.280, B:F.308, B:F.336, B:L.344 Hydrogen bonds: B:F.338, B:F.338 Water bridges: B:R.285, B:H.341 Salt bridges: B:H.86, B:R.90, B:R.285, B:H.341 pi-Stacking: B:F.336 Metal complexes: B:C.343

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

SO4.4: 3 residues within 4Å: Chain A: R.24, E.25, R.28 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.25 Water bridges: A:R.24, A:R.24, A:R.24, A:D.322 Salt bridges: A:R.28 SO4.5: 2 residues within 4Å: Chain A: R.239, R.378 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.236, A:R.239, A:R.378, A:R.378 Salt bridges: A:R.239, A:R.378 SO4.6: 5 residues within 4Å: Chain A: T.2, Q.3, M.4, R.7, W.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.4 Water bridges: A:R.7, A:E.34 Salt bridges: A:R.7 SO4.9: 2 residues within 4Å: Chain B: R.24, R.28 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.24, B:R.24, B:R.24, B:R.24, B:E.25 Salt bridges: B:R.28 SO4.10: 3 residues within 4Å: Chain B: E.236, R.239, R.378 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.239, B:R.378 Salt bridges: B:R.239, B:R.378 SO4.11: 5 residues within 4Å: Chain B: T.2, Q.3, M.4, R.7, W.29 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.2, B:M.4 Water bridges: B:R.7, B:E.34 Salt bridges: B:R.7

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

EDO.7: 4 residues within 4Å: Chain A: G.233, T.237, M.283 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: I.79, G.233, M.283 Ligands: HEM.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Fernandez, E. et al., A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway. Environ.Microbiol. (2013)

Release Date

2013-02-27

Peptides

P450 HEME-THIOLATE PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

P450 HEME-THIOLATE PROTEIN

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