MolNFT v1 · #145967 · protein
FTV7 dioxygenase with 2,4-D bound
6D3I: “FTV7 dioxygenase with 2,4-D bound”. X-ray diffraction, 3 ligands (AKG, CFA, CO), 17 pockets (best druggability 0.79). MolNFT v1 #145967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D3I
- Type
- protein
- Length
- 1,141 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FTV7 dioxygenase
- Ligands
- AKG, CFA, CO
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FTV7 dioxygenase | protein | 286 | 21% helix, 25% strand | — |
| G, D, J | FTV7 dioxygenase | protein | 285 | 22% helix, 28% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, G, D, J
- CFA · (2,4-dichlorophenoxy)acetic acid · ligand · 2 copies · chains G, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, G, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.79 | 0.91 | 46 | CO, AKG, CFA |
| 2 | 319 | 0.77 | 0.88 | 48 | CO, AKG |
| 3 | 253 | 0.76 | 0.89 | 37 | CO, AKG |
| 4 | 227 | 0.75 | 0.90 | 42 | CO, AKG, CFA |
| 5 | 346 | 0.60 | 0.77 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1082 Ų buried · 9 hydrogen bonds · protein-protein
- G–J · 1020 Ų buried · 11 hydrogen bonds · protein-protein
- D–J · 284 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 159 Ų buried · 6 hydrogen bonds · protein-protein
- G–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6D3I · ftv7 dioxygenase with 2,4-D bound · 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
- Elsewhere: RCSB PDB 6D3I · PDBe 6D3I
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