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The crystal structure of the orthorhombic form of biotin protein ligase from pyrococcus horikoshii OT3 in complex with biotin and ADP
Analyse The crystal structure of the orthorhombic form of biotin protein ligase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DTH
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
- EC
- 6.3.4.15
- UniProt
- O57883
- Ligands
- ADP, BTN
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15) | protein | 235 | 26% helix, 32% 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 | 251 | 0.63 | 0.82 | 41 | ADP, BTN |
| 2 | 271 | 0.63 | 0.81 | 43 | ADP, BTN |
| 3 | 138 | 0.47 | 0.77 | 22 | empty |
| 4 | 99 | 0.41 | 0.76 | 19 | empty |
| 5 | 53 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 995 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2DTH · The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus… · 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 2DTH · PDBe 2DTH · UniProt O57883
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