SMTL ID : 7zs4.1

F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain A: H.91 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.91, H2O.3

2 x HEC: HEME C(Covalent)

HEC.2: 19 residues within 4Å: Chain A: K.38, M.40, H.56, V.58, L.79, F.81, G.102, V.103, M.104, Y.119, E.120, V.132, C.139, C.142, H.143, V.152, F.153, S.154 Ligands: PEG.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:V.58, A:L.79, A:F.81, A:F.81, A:Y.119, A:V.132, A:F.153, A:F.153, A:F.153 Hydrogen bonds: A:Y.151, A:F.153, A:S.154 Water bridges: A:K.38 Salt bridges: A:K.38, A:H.56, A:H.143 pi-Stacking: A:Y.119, A:F.153 Metal complexes: A:H.143 HEC.4: 18 residues within 4Å: Chain B: K.38, M.40, H.56, L.79, F.81, G.102, V.103, M.104, E.120, V.132, G.138, C.139, C.142, H.143, V.152, F.153, S.154 Ligands: PEG.6 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:F.81, B:F.81, B:V.132, B:F.153, B:F.153, B:F.153 Hydrogen bonds: B:F.153, B:S.154 Water bridges: B:K.38 Salt bridges: B:K.38, B:H.56, B:H.143 pi-Stacking: B:F.81, B:F.153 Metal complexes: B:H.143

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: V.52, F.81, L.100, G.102 Ligands: HEC.2 No protein-ligand interaction detected (PLIP) PEG.6: 5 residues within 4Å: Chain B: V.52, F.81, L.100, G.102 Ligands: HEC.4 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.27, F.31, R.98, E.124, G.125 Chain B: D.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.27, A:R.98, A:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, H.R. et al., A heme pocket aromatic quadrupole modulates gas binding to cytochrome c'-beta : Implications for NO sensors. J.Biol.Chem. (2023)

Release Date

2023-05-17

Peptides

Cytochrome c: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c

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