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Non-oxidized yfir

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

PDB: 4YN7
Type: protein
Length: 301 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yfir
UniProt: Q9I4L4
Ligands: SO4
Pockets: 6 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yfir	protein	153	33% helix, 24% strand	Q9I4L4
B	Yfir	protein	148	32% helix, 25% strand	Q9I4L4

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.47	0.83	14	empty
2	102	0.47	0.80	21	empty
3	156	0.42	0.74	32	SO4
4	109	0.41	0.76	16	empty
5	102	0.40	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 745 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 disulfide (engineered, disulfide).

Compared structures

4YN7 · Non-oxidized YfiR · 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 Q9I4L4
Elsewhere: RCSB PDB 4YN7 · PDBe 4YN7 · UniProt Q9I4L4

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