Research workbench
Crystal structure of the biotin protein ligase (mutations R48A and K111A) and biotin carboxyl carrier protein complex from pyrococcus horikoshii OT3
Analyse Crystal structure of the biotin protein ligase (mutations R48A and K111A) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EJF
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase; 149AA long hypothetical…
- UniProt
- O57883, O59021
- Ligands
- BTN, ADN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase | protein | 235 | 26% helix, 34% strand | O57883 |
| B | 235AA long hypothetical biotin--[acetyl-CoA-carboxylase] ligase | protein | 227 | 28% helix, 33% strand | O57883 |
| C, D | 149AA long hypothetical methylmalonyl-CoA decarboxylase gamma chain | protein | 69 | 0% helix, 51% strand | O59021 |
Ligands and binding sites
- BTN · Biotin · ligand · 3 copies · chains A, B, C
- ADN · Adenosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 297 | 0.65 | 0.81 | 63 | BTN, ADN |
| 2 | 230 | 0.62 | 0.81 | 43 | BTN, ADN |
| 3 | 92 | 0.42 | 0.78 | 15 | BTN |
| 4 | 93 | 0.41 | 0.77 | 22 | empty |
| 5 | 61 | 0.38 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1072 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 992 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (biotinylation).
Compared structures
- 2EJF · Crystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin… · the same entry in another collection · chain B against B, 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
- Every structure of UniProt O59021
- Elsewhere: RCSB PDB 2EJF · PDBe 2EJF · UniProt O57883 · UniProt O59021
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