MolNFT v1 · #19530 · protein

Cytochrome ch from methylobacterium extorquens

1QN2: “Cytochrome ch from methylobacterium extorquens”. X-ray diffraction, 1 ligand (HEC), 5 pockets (best druggability 0.75). MolNFT v1 #19530 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QN2
Type: protein
Length: 295 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome ch
Ligands: HEC
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome ch	protein	99	44% helix, 2% strand	—
B, C	Cytochrome ch	protein	98	45% helix, 2% strand	—

Ligands and binding sites

HEC · Heme C · ligand · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.75	0.88	40	HEC
2	236	0.74	0.88	38	HEC
3	230	0.74	0.88	40	HEC
4	577	0.64	0.75	50	empty
5	152	0.43	0.75	21	empty

Interfaces

3 interfaces between chains.

A–B · 178 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 114 Å² buried · 1 hydrogen bond · protein-protein
B–C · 92 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (heme c attachment).

Compared structures

1QN2 · cytochrome cH from Methylobacterium extorquens · 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 1QN2 · PDBe 1QN2

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