Research workbench
Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in complex with ADP and biotin
Analyse Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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