MolNFT v1 · #140294 · protein

Yfir complexed with gmp

5Y62: “Yfir complexed with gmp”. X-ray diffraction, 1 ligand (5GP), 6 pockets (best druggability 0.47). MolNFT v1 #140294 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Y62
Type: protein
Length: 301 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yfir
UniProt: Q9I4L4
Ligands: 5GP
Pockets: 6 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yfir	protein	153	35% helix, 24% strand	Q9I4L4
B	Yfir	protein	148	28% helix, 25% strand	Q9I4L4

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · chains 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	75	0.47	0.83	18	empty
2	99	0.43	0.78	20	empty
3	170	0.43	0.74	25	empty
4	107	0.41	0.77	17	empty
5	81	0.35	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 766 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5Y62 · YfiR complexed with GMP · 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
Every structure of UniProt Q9I4L4
Elsewhere: RCSB PDB 5Y62 · PDBe 5Y62 · UniProt Q9I4L4

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