MolNFT v1 · #102240 · protein

Crystal structure of arabidopsis thaliana dj-1D

4OFW · Protein dj-1 homolog D: “Crystal structure of arabidopsis thaliana dj-1D”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #102240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OFW
Type: protein
Length: 2,322 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein dj-1 homolog D
EC: 4.2.1.130
UniProt: Q9M8R4
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein dj-1 homolog D (EC 4.2.1.130)	protein	387	33% helix, 25% strand	Q9M8R4

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.74	0.94	31	empty
2	64	0.72	0.98	23	empty
3	54	0.70	0.98	22	empty
4	61	0.70	0.97	22	empty
5	95	0.68	0.92	29	empty

Interfaces

7 interfaces between chains.

D–F · 1290 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1283 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1274 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1272 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1256 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4OFW · Crystal Structure of Arabidopsis thaliana DJ-1d · the same entry in another collection · chain F against F, TM-score 1.00
Q9M8R4 · AlphaFold monomer V2.0 prediction for protein dj-1 homolog D (Q9M8R4) · a predicted model of the same protein · chain D 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 Q9M8R4
Elsewhere: RCSB PDB 4OFW · PDBe 4OFW · UniProt Q9M8R4

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