MolNFT v1 · #102258 · protein
Crystal structure of arabidopsis thaliana dj-1D with glyoxylate as substrate analog
4OGG · Protein dj-1 homolog D: “Crystal structure of arabidopsis thaliana dj-1D with glyoxylate as substrate analog”. X-ray diffraction, 13 pockets (best druggability 0.73). MolNFT v1 #102258 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4OGG
- Type
- protein
- Length
- 1,161 residues
- Chains
- 3
- 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
- 13 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dj-1 homolog D (EC 4.2.1.130) | protein | 386 | 34% helix, 25% strand | Q9M8R4 |
| B | Protein dj-1 homolog D (EC 4.2.1.130) | protein | 387 | 36% helix, 26% strand | Q9M8R4 |
| C | Protein dj-1 homolog D (EC 4.2.1.130) | protein | 388 | 35% helix, 26% strand | Q9M8R4 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.73 | 0.94 | 31 | empty |
| 2 | 60 | 0.72 | 0.98 | 24 | empty |
| 3 | 120 | 0.68 | 0.90 | 37 | empty |
| 4 | 624 | 0.63 | 0.74 | 57 | empty |
| 5 | 145 | 0.43 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1263 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1251 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1248 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 4OGG · Crystal Structure of Arabidopsis thaliana DJ-1d with glyoxylate as substrate analog · the same entry in another collection · chain A against A, 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 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 Q9M8R4
- Elsewhere: RCSB PDB 4OGG · PDBe 4OGG · UniProt Q9M8R4
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