Research workbench

Trimeric heme-free cytochrome variant apocyt-TRICYT3

Analyse Trimeric heme-free cytochrome variant apocyt-TRICYT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8DEL
Type: protein
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
Ligands: MG, ZN
Pockets: 6 · best druggability 0.75

Structure

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

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

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
ZN · Zinc ion · metal · chains A, B, C

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

Pockets

6 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	78	0.75	0.98	21	empty
2	236	0.56	0.78	39	empty
3	221	0.54	0.77	40	MG
4	117	0.45	0.78	21	empty
5	124	0.45	0.77	24	empty

Interfaces

3 interfaces between chains.

A–C · 670 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 664 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 636 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

8DEL · Trimeric Heme-Free Cytochrome Variant ApoCyt-TriCyt3 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8DEL · PDBe 8DEL

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