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1.25A resolution structure of rat type B cytochrome B5

Analyse 1.25A resolution structure of rat type B cytochrome B5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HIL
Type: protein
Length: 166 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B5 type B
UniProt: P04166
Ligands: HEM, NA
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome B5 type B	protein	85	35% helix, 24% strand	P04166
B	Cytochrome B5 type B	protein	81	41% helix, 25% strand	P04166

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.71	0.92	28	empty
2	125	0.63	0.86	20	HEM
3	118	0.62	0.86	20	HEM
4	70	0.33	0.76	19	empty
5	62	0.33	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 650 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4HIL · 1.25A Resolution Structure of Rat Type B Cytochrome b5 · the same entry in another collection · chain A against A, TM-score 1.00
P04166 · AlphaFold monomer V2.0 prediction for cytochrome B5 type B (P04166) · a predicted model of the same protein · chain B 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 P04166
Elsewhere: RCSB PDB 4HIL · PDBe 4HIL · UniProt P04166

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