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FE(II)-bound structure of the engineered cyt CB562 variant, CH3

Analyse FE(II)-bound structure of the engineered cyt CB562 variant, CH3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DYE
Type: protein
Length: 212 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: HEC, FE, CA
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Soluble cytochrome B562	protein	106	82% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · chains A, B
CA · Calcium ion · metal · chains A

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

Pockets

3 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	411	0.67	0.80	44	HEC
2	258	0.66	0.83	40	HEC
3	84	0.35	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 490 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 1 disulfide (heme c attachment, disulfide).

Compared structures

6DYE · Fe(II)-bound structure of the engineered cyt cb562 variant, CH3 · the same entry in another collection · chain A against A, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 6DYE · PDBe 6DYE · UniProt P0ABE7

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