MolNFT v1 · #18093 · protein

Crystal structure of human dj-1, P 1 21 1 space group

1PDW: “Crystal structure of human dj-1, P 1 21 1 space group”. X-ray diffraction, 15 pockets (best druggability 0.64). MolNFT v1 #18093 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PDW
Type: protein
Length: 1,502 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dj-1
UniProt: Q99497
Pockets: 15 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, H	Dj-1	protein	187	40% helix, 21% strand	Q99497
E	Dj-1	protein	189	41% helix, 21% strand	Q99497
G	Dj-1	protein	191	41% helix, 20% strand	Q99497

Pockets

15 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	384	0.64	0.78	48	empty
2	198	0.53	0.78	34	empty
3	132	0.52	0.80	23	empty
4	136	0.52	0.80	21	empty
5	120	0.52	0.81	23	empty

Interfaces

7 interfaces between chains.

G–H · 1364 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1363 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1353 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1328 Å² buried · 24 hydrogen bonds · protein-protein
C–G · 278 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

1PDW · Crystal structure of human DJ-1, P 1 21 1 space group · the same entry in another collection · chain H against H, TM-score 1.00
Q99497 · AlphaFold monomer V2.0 prediction for parkinson disease protein 7 (Q99497) · a predicted model of the same protein · 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 Q99497
Elsewhere: RCSB PDB 1PDW · PDBe 1PDW · UniProt Q99497

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