MolNFT v1 · #37349 · protein
Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in complex with ADP and biotin
2FYK · Biotin--protein ligase: “Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in complex with ADP and biotin”. X-ray diffraction, 2 ligands (ADP, BTN), 6 pockets (best druggability 0.66). MolNFT v1 #37349 on…
- PDB
- 2FYK
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biotin--protein ligase
- EC
- 6.3.4.15
- UniProt
- O57883
- Ligands
- ADP, BTN
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Biotin--protein ligase (EC 6.3.4.15) | protein | 235 | 28% helix, 31% strand | O57883 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BTN · Biotin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.66 | 0.82 | 46 | ADP, BTN |
| 2 | 237 | 0.61 | 0.81 | 37 | ADP, BTN |
| 3 | 131 | 0.42 | 0.75 | 28 | empty |
| 4 | 89 | 0.40 | 0.77 | 17 | empty |
| 5 | 53 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1061 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2FYK · Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in complex with… · 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 O57883
- Elsewhere: RCSB PDB 2FYK · PDBe 2FYK · UniProt O57883
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