MolNFT v1 · #23746 · protein

Crystal structure of F58W mutant of cytochrome B5

1U9M: “Crystal structure of F58W mutant of cytochrome B5”. X-ray diffraction, 1 ligand (HEM), 10 pockets (best druggability 0.79). MolNFT v1 #23746 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1U9M
Type: protein
Length: 492 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B5
UniProt: P00171
Ligands: HEM
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cytochrome B5	protein	82	40% helix, 27% strand	P00171

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.79	0.85	51	HEM
2	493	0.76	0.84	53	HEM
3	123	0.62	0.86	20	HEM
4	137	0.62	0.85	20	HEM
5	126	0.62	0.85	20	HEM

Interfaces

8 interfaces between chains.

A–F · 473 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 433 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 415 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 405 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 346 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1U9M · Crystal structure of F58W mutant of cytochrome b5 · the same entry in another collection · chain F against F, TM-score 1.00
P00171 · AlphaFold monomer V2.0 prediction for cytochrome B5 (P00171) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P00171
Elsewhere: RCSB PDB 1U9M · PDBe 1U9M · UniProt P00171

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