MolNFT v1 · #45926 · protein
Crystal structure of a dioxygenase in the crotonase superfamily
2NP9 · Dpgc: “Crystal structure of a dioxygenase in the crotonase superfamily”. X-ray diffraction, 2 ligands (YE1, OXY), 19 pockets (best druggability 0.83). MolNFT v1 #45926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NP9
- Type
- protein
- Length
- 1,266 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dpgc
- EC
- 1.13.11.-
- UniProt
- Q8KLK7
- Ligands
- YE1, OXY
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dpgc (EC 1.13.11.-) | protein | 423 | 54% helix, 13% strand | Q8KLK7 |
| B | Dpgc (EC 1.13.11.-) | protein | 422 | 55% helix, 13% strand | Q8KLK7 |
| C | Dpgc (EC 1.13.11.-) | protein | 421 | 54% helix, 13% strand | Q8KLK7 |
Ligands and binding sites
- YE1 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-4-({3-[(2-{[(3,5-dihydroxyphenyl)acetyl]amino}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 3 copies · chains A, B, C
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.83 | 0.85 | 71 | empty |
| 2 | 204 | 0.69 | 0.86 | 33 | OXY |
| 3 | 315 | 0.68 | 0.82 | 45 | YE1, OXY |
| 4 | 300 | 0.68 | 0.82 | 41 | YE1, OXY |
| 5 | 584 | 0.67 | 0.77 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1464 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1460 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1446 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2NP9 · Crystal structure of a dioxygenase in the Crotonase superfamily · the same entry in another collection · chain A against A, TM-score 1.00
- Q8KLK7 · AlphaFold monomer V2.0 prediction for (3,5-DIHYDROXYPHENYL)ACETYL-CoA 1,2-dioxygenase… · a predicted model of the same protein · chain B 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 Q8KLK7
- Elsewhere: RCSB PDB 2NP9 · PDBe 2NP9 · UniProt Q8KLK7
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