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N-butylisocyanide bound rhodobacter capsulatus cytochrome C'

Analyse N-butylisocyanide bound rhodobacter capsulatus cytochrome C' in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NBB
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C'
UniProt: P00147
Ligands: HEM, NBN
Pockets: 4 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome C'	protein	129	74% helix, 2% strand	P00147

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NBN · N-butyl isocyanide · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.74	0.85	40	HEM, NBN
2	326	0.73	0.85	33	HEM, NBN
3	225	0.49	0.75	33	empty
4	57	0.37	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 537 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1NBB · N-butylisocyanide bound rhodobacter capsulatus cytochrome C' · the same entry in another collection · chain A against A, TM-score 1.00
P00147 · AlphaFold monomer V2.0 prediction for cytochrome C' (P00147) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00147
Elsewhere: RCSB PDB 1NBB · PDBe 1NBB · UniProt P00147

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