MolNFT v1 · #51193 · protein

Structure of wild-type phormidium laminosum cytochrome C6

2V08: “Structure of wild-type phormidium laminosum cytochrome C6”. X-ray diffraction, 3 ligands (HEC, ZN, CL), 1 pocket (best druggability 0.82). MolNFT v1 #51193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2V08
Type: protein
Length: 168 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C6
Ligands: HEC, ZN, CL
Pockets: 1 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome C6	protein	84	61% helix, 2% strand	—

Ligands and binding sites

HEC · Heme C · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 9 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A
IMD · Imidazole · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	544	0.82	0.88	70	HEC

Interfaces

1 interface between chains.

A–B · 270 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (heme c attachment).

Compared structures

2V08 · Structure of wild-type Phormidium laminosum cytochrome c6 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2V08 · PDBe 2V08

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