MolNFT v1 · #174280 · protein
The crystal structure of pdxi complex with the alder-ene adduct
7BQL · METHYLTRANSF_2 domain-containing protein: “The crystal structure of pdxi complex with the alder-ene adduct”. X-ray diffraction, 1 ligand (F5F), 12 pockets (best druggability 0.87). MolNFT v1 #174280 on GenesisL1: 3D structure…
- PDB
- 7BQL
- Type
- protein
- Length
- 905 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- METHYLTRANSF_2 domain-containing protein
- UniProt
- A0A1F8A906
- Ligands
- F5F
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | METHYLTRANSF_2 domain-containing protein | protein | 447 | 50% helix, 13% strand | A0A1F8A906 |
| B | METHYLTRANSF_2 domain-containing protein | protein | 458 | 50% helix, 14% strand | A0A1F8A906 |
Ligands and binding sites
- F5F · 3-[(1R,2S,4R,6S)-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1H-pyridin-2-one · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.87 | 0.95 | 41 | empty |
| 2 | 561 | 0.83 | 0.88 | 53 | F5F |
| 3 | 560 | 0.82 | 0.88 | 57 | F5F |
| 4 | 357 | 0.62 | 0.78 | 29 | empty |
| 5 | 317 | 0.62 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 5564 Ų buried · 97 hydrogen bonds · protein-protein
Compared structures
- 7BQL · The crystal structure of PdxI complex with the Alder-ene adduct · 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 A0A1F8A906
- Elsewhere: RCSB PDB 7BQL · PDBe 7BQL · UniProt A0A1F8A906
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