SMTL ID : 7zqz.1

F61V Cytochrome c prime beta from Methylococcus capsulatus (Bath): NO complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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: 23 residues within 4Å: Chain A: K.38, M.40, L.48, F.52, H.56, V.58, L.79, V.81, G.102, V.103, M.104, Y.119, E.120, V.132, G.138, C.139, C.142, H.143, V.152, F.153, S.154 Ligands: NO.3, PEG.4 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.48, A:V.58, A:V.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 Salt bridges: A:K.38, A:H.56, A:H.143 pi-Stacking: A:F.153 Metal complexes: A:H.143 HEC.5: 22 residues within 4Å: Chain B: K.38, M.40, L.48, F.52, H.56, L.79, V.81, G.102, V.103, M.104, Y.119, E.120, V.132, G.138, C.139, C.142, H.143, V.152, F.153, S.154 Ligands: NO.8, PEG.9 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.48, B:V.81, B:V.81, B:Y.119, 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.153 Metal complexes: NO.8

2 x NO: NITRIC OXIDE(Non-covalent)

NO.3: 4 residues within 4Å: Chain A: F.52, V.81 Ligands: HEC.2, PEG.4 No protein-ligand interaction detected (PLIP) NO.8: 4 residues within 4Å: Chain B: F.52, V.81 Ligands: HEC.5, PEG.9 No protein-ligand interaction detected (PLIP)

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

PEG.4: 4 residues within 4Å: Chain A: P.51, F.52 Ligands: HEC.2, NO.3 No protein-ligand interaction detected (PLIP) PEG.9: 5 residues within 4Å: Chain B: N.50, P.51, F.52 Ligands: HEC.5, NO.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.50

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: Y.27, F.31, R.98, G.125 Chain B: D.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.27 Water bridges: A:G.30 GOL.7: 6 residues within 4Å: Chain A: D.158 Chain B: Y.27, D.29, G.30, F.31, R.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.27, B:Y.27, B:G.30, B:R.32

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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