Research workbench
Crystal structure of arabidopsis thaliana hppd complexed with ntbc
Analyse Crystal structure of arabidopsis thaliana hppd complexed with ntbc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J63
- Type
- protein
- Length
- 1,472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- EC
- 1.13.11.27
- UniProt
- P93836
- Ligands
- NTD, FE
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 367 | 25% helix, 34% strand | P93836 |
| B, D | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 370 | 25% helix, 33% strand | P93836 |
| C | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 365 | 25% helix, 34% strand | P93836 |
Ligands and binding sites
- NTD · 2-{hydroxy[2-nitro-4-(trifluoromethyl) phenyl]methylene}cyclohexane-1,3-dione · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.72 | 0.81 | 43 | empty |
| 2 | 572 | 0.72 | 0.80 | 53 | NTD |
| 3 | 83 | 0.71 | 0.95 | 36 | empty |
| 4 | 544 | 0.70 | 0.79 | 55 | FE, NTD |
| 5 | 536 | 0.70 | 0.79 | 52 | NTD |
Interfaces
4 interfaces between chains.
- C–D · 1571 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1556 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6J63 · Crystal structure of Arabidopsis thaliana HPPD complexed with NTBC · the same entry in another collection · 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 P93836
- Elsewhere: RCSB PDB 6J63 · PDBe 6J63 · UniProt P93836
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.