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M.ACETIVORANS protoglobin F93Y mutant in complex with cyanide

Analyse M.ACETIVORANS protoglobin F93Y mutant in complex with cyanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZOL
Type: protein
Length: 382 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protoglobin
UniProt: Q8TLY9
Ligands: HEM, CYN, SO4
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protoglobin	protein	191	65% helix, 2% strand	Q8TLY9

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
CYN · Cyanide ion · ion · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

2 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	317	0.86	0.96	38	HEM, CYN
2	311	0.86	0.96	38	HEM, CYN

Interfaces

1 interface between chains.

A–B · 1939 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

3ZOL · M.acetivorans protoglobin F93Y mutant in complex with cyanide · the same entry in another collection · chain B against B, 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
Every structure of UniProt Q8TLY9
Elsewhere: RCSB PDB 3ZOL · PDBe 3ZOL · UniProt Q8TLY9

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