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Crystal structure of biotin protein ligase from pyrococcus horikoshii OT3 in complex with biotinyl-5'-AMP, pyrophosphate and MG(2+)
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
- 2DKG
- 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
- BT5, POP, MG
- Pockets
- 6 · best druggability 0.60
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
- BT5 · Biotinyl-5-amp · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · chains A
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 | 200 | 0.60 | 0.82 | 40 | MG, POP, BT5 |
| 2 | 208 | 0.60 | 0.81 | 35 | BT5 |
| 3 | 101 | 0.42 | 0.77 | 20 | empty |
| 4 | 99 | 0.40 | 0.76 | 17 | empty |
| 5 | 63 | 0.38 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1046 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2DKG · 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 2DKG · PDBe 2DKG · UniProt O57883
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