Research workbench

ATVAL1 phd-like domain in the P31 space group

Analyse ATVAL1 phd-like domain in the P31 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YUG
Type: protein
Length: 388 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B3 domain-containing transcription repressor VAL1
UniProt: Q8W4L5
Ligands: ZN
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	B3 domain-containing transcription repressor VAL1	protein	92	25% helix, 23% strand	Q8W4L5
E, G	B3 domain-containing transcription repressor VAL1	protein	102	22% helix, 19% strand	Q8W4L5

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, E, G
GOL · Glycerol · additive · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	400	0.70	0.81	47	empty
2	214	0.61	0.81	42	GOL
3	177	0.47	0.76	34	empty
4	51	0.43	0.83	20	GOL

Interfaces

4 interfaces between chains.

B–E · 1322 Å² buried · 20 hydrogen bonds · protein-protein
B–G · 603 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 304 Å² buried · 0 hydrogen bonds · protein-protein
A–E · 189 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5YUG · AtVAL1 PHD-Like domain in the P31 space group · the same entry in another collection · chain A against A, TM-score 1.00
Q8W4L5 · AlphaFold monomer V2.0 prediction for B3 domain-containing transcription repressor VAL1… · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q8W4L5
Elsewhere: RCSB PDB 5YUG · PDBe 5YUG · UniProt Q8W4L5

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