MolNFT v1 · #129415 · protein

YCF48 bound to D1 peptide

5OJP · YCF48-like protein: “YCF48 bound to D1 peptide”. X-ray diffraction, 6 pockets (best druggability 0.84). MolNFT v1 #129415 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OJP
Type: protein
Length: 910 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YCF48-like protein
UniProt: Q8DI95
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 1% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YCF48-like protein	protein	309	1% helix, 47% strand	Q8DI95
B	YCF48-like protein	protein	302	1% helix, 47% strand	Q8DI95
C	YCF48-like protein	protein	299	2% helix, 47% strand	Q8DI95

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.84	0.85	97	empty
2	413	0.81	0.89	55	empty
3	337	0.79	0.89	44	empty
4	98	0.57	0.86	24	empty
5	217	0.52	0.77	41	empty

Interfaces

3 interfaces between chains.

A–B · 748 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 459 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 272 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5OJP · YCF48 bound to D1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q8DI95 · AlphaFold monomer V2.0 prediction for YCF48-like protein (Q8DI95) · a predicted model of the same protein · chain B 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 Q8DI95
Elsewhere: RCSB PDB 5OJP · PDBe 5OJP · UniProt Q8DI95

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