MolNFT v1 · #146968 · protein

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

6DYD · Soluble cytochrome B562: “CU(II)-bound structure of the engineered cyt CB562 variant, CH3”. X-ray diffraction, 3 ligands (HEC, CA, CU), 3 pockets (best druggability 0.66). MolNFT v1 #146968 on GenesisL1: 3D structure, binding sites…

PDB: 6DYD
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, CA, CU
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Soluble cytochrome B562	protein	106	78% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 2 copies · chains A, C
CA · Calcium ion · metal · 5 copies · chains A, C
CU · Copper (II) ion · metal · chains A, C

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

Pockets

3 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	201	0.66	0.85	31	HEC
2	262	0.59	0.79	28	empty
3	155	0.57	0.82	23	HEC

Interfaces

1 interface between chains.

A–C · 508 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6DYD · Cu(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 C 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 6DYD · PDBe 6DYD · UniProt P0ABE7

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