Research workbench
Crystal structure of acka from mycobacterium paratuberculosis atcc baa-968 / K-10
Analyse Crystal structure of acka from mycobacterium paratuberculosis atcc baa-968 /… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9P
- Type
- protein
- Length
- 759 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acka
- UniProt
- Q73T33
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acka | protein | 380 | 42% helix, 19% strand | Q73T33 |
| B | Acka | protein | 379 | 43% helix, 18% strand | Q73T33 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.78 | 0.80 | 96 | empty |
| 2 | 912 | 0.75 | 0.79 | 92 | PGE |
| 3 | 461 | 0.63 | 0.77 | 51 | PGE |
| 4 | 180 | 0.46 | 0.75 | 22 | empty |
| 5 | 184 | 0.45 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1140 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3R9P · Crystal structure of AckA from Mycobacterium paratuberculosis ATCC BAA-968 / K-10 · the same entry in another collection · chain A against A, TM-score 1.00
- Q73T33 · AlphaFold monomer V2.0 prediction for acetate kinase (Q73T33) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q73T33
- Elsewhere: RCSB PDB 3R9P · PDBe 3R9P · UniProt Q73T33
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