Research workbench
The structure of pdxi in complex with its substrate analogue
Analyse The structure of pdxi in complex with its substrate analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BQK
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- METHYLTRANSF_2 domain-containing protein
- UniProt
- A0A1F8A906
- Ligands
- F56
- Pockets
- 12 · best druggability 0.86
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 | 459 | 51% helix, 13% strand | A0A1F8A906 |
| B | METHYLTRANSF_2 domain-containing protein | protein | 451 | 49% helix, 13% strand | A0A1F8A906 |
Ligands and binding sites
- F56 · 3-[(E,2S,4S)-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1H-pyridin-2-one · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 4 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.86 | 0.95 | 36 | GOL |
| 2 | 591 | 0.84 | 0.89 | 59 | F56, EDO, GOL |
| 3 | 591 | 0.84 | 0.89 | 60 | F56, EDO, GOL |
| 4 | 422 | 0.62 | 0.76 | 39 | empty |
| 5 | 297 | 0.62 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 5542 Ų buried · 87 hydrogen bonds · protein-protein
Compared structures
- 7BQK · The structure of PdxI in complex with its substrate analogue · 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 7BQK · PDBe 7BQK · UniProt A0A1F8A906
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