MolNFT v1 · #191366 · protein

Heme-free cytochrome variant apocyt

8DEN · Soluble cytochrome B562: “Heme-free cytochrome variant apocyt”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #191366 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8DEN
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
Pockets: 5 · best druggability 0.68

Structure

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	729	0.68	0.76	76	empty
2	52	0.46	0.85	12	empty
3	98	0.38	0.75	20	empty
4	70	0.37	0.78	13	empty
5	83	0.31	0.73	13	empty

Interfaces

4 interfaces between chains.

A–B · 836 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 543 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 474 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 356 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

8DEN · Heme-Free Cytochrome Variant ApoCyt · the same entry in another collection · chain D against D, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 8DEN · PDBe 8DEN · UniProt P0ABE7

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