MolNFT v1 · #129416 · protein

YCF48 bound to D1 peptide

5OJR · YCF48-like protein: “YCF48 bound to D1 peptide”. X-ray diffraction, 11 pockets (best druggability 0.85). MolNFT v1 #129416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OJR
Type: protein
Length: 1,257 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YCF48-like protein; Photosystem II protein D1 3
EC: 1.10.3.9
UniProt: Q8DI95, Q8DIV4
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YCF48-like protein	protein	308	1% helix, 48% strand	Q8DI95
B	YCF48-like protein	protein	310	2% helix, 48% strand	Q8DI95
C	YCF48-like protein	protein	301	1% helix, 48% strand	Q8DI95
D	YCF48-like protein	protein	303	2% helix, 48% strand	Q8DI95
E	Photosystem II protein D1 3 (EC 1.10.3.9)	protein	18	0% helix, 44% strand	Q8DIV4
F	Photosystem II protein D1 3 (EC 1.10.3.9)	protein	17	24% helix, 35% strand	Q8DIV4

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1125	0.85	0.86	123	empty
2	655	0.83	0.87	67	empty
3	548	0.81	0.87	49	empty
4	187	0.54	0.79	35	empty
5	137	0.54	0.82	31	empty

Interfaces

9 interfaces between chains.

A–E · 1078 Å² buried · 22 hydrogen bonds · protein-protein
B–F · 854 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 832 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 822 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 293 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5OJR · YCF48 bound to D1 peptide · the same entry in another collection · chain F against F, TM-score 1.00
Q8DI95 · AlphaFold monomer V2.0 prediction for YCF48-like protein (Q8DI95) · a predicted model of the same protein · chain D against A, TM-score 0.99
Q8DIV4 · AlphaFold monomer V2.0 prediction for photosystem II protein D1 3 (Q8DIV4) · a predicted model of the same protein · chain F against A, TM-score 0.22

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
Every structure of UniProt Q8DIV4
Elsewhere: RCSB PDB 5OJR · PDBe 5OJR · UniProt Q8DI95 · UniProt Q8DIV4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.