MolNFT v1 · #146974 · protein

Iron-bound structure of the engineered cyt B562 variant, CH3Y*

6DYJ · Soluble cytochrome B562: “Iron-bound structure of the engineered cyt B562 variant, CH3Y*”. X-ray diffraction, 2 ligands (FE, MG), 7 pockets (best druggability 0.73). MolNFT v1 #146974 on GenesisL1: 3D structure, binding sites and…

PDB: 6DYJ
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: FE, MG
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Soluble cytochrome B562	protein	106	79% helix, 0% strand	P0ABE7

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains A, E, C, G
MG · Magnesium ion · metal · chains E

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

Pockets

7 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	724	0.73	0.79	74	empty
2	354	0.65	0.80	29	empty
3	192	0.56	0.80	30	empty
4	95	0.41	0.78	20	empty
5	53	0.35	0.78	13	empty

Interfaces

4 interfaces between chains.

A–E · 557 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 535 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 494 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 34 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6DYJ · Iron-bound structure of the engineered cyt b562 variant, CH3Y* · the same entry in another collection · chain C against C, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 P0ABE7
Elsewhere: RCSB PDB 6DYJ · PDBe 6DYJ · UniProt P0ABE7

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