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Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in complex with biotinyl-5'-AMP, K111G mutation
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
- 2DEQ
- Type
- protein
- Length
- 469 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
- BT5
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15) | protein | 235 | 28% helix, 31% strand | O57883 |
| B | 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15) | protein | 234 | 28% helix, 29% strand | O57883 |
Ligands and binding sites
- BT5 · Biotinyl-5-amp · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.64 | 0.81 | 45 | BT5 |
| 2 | 272 | 0.61 | 0.80 | 40 | BT5 |
| 3 | 201 | 0.49 | 0.75 | 26 | empty |
| 4 | 109 | 0.44 | 0.77 | 18 | empty |
| 5 | 88 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1015 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2DEQ · 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 2DEQ · PDBe 2DEQ · UniProt O57883
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