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Cytoglobin cavities

Analyse Cytoglobin cavities in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1URY
Type: protein
Length: 308 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytoglobin
UniProt: Q8WWM9
Ligands: HEM, FC6, XE
Pockets: 4 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytoglobin	protein	154	79% helix, 0% strand	Q8WWM9

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
FC6 · Hexacyanoferrate(3-) · ligand · 2 copies · chains A, B
XE · Xenon · ion · 7 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	266	0.77	0.88	39	HEM, XE
2	295	0.75	0.86	41	HEM, XE
3	331	0.59	0.77	41	FC6
4	276	0.58	0.78	33	FC6

Interfaces

1 interface between chains.

A–B · 771 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1URY · cytoglobin cavities · the same entry in another collection · chain A against A, TM-score 1.00
Q8WWM9 · AlphaFold monomer V2.0 prediction for cytoglobin (Q8WWM9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8WWM9
Elsewhere: RCSB PDB 1URY · PDBe 1URY · UniProt Q8WWM9

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