MolNFT v1 · #74031 · protein
Crystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis
3OKS: “Crystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.65). MolNFT v1 #74031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OKS
- Type
- protein
- Length
- 1,783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate transaminase
- EC
- 2.6.1.19
- UniProt
- A0QWJ0
- Ligands
- MG
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 444 | 40% helix, 18% strand | A0QWJ0 |
| B | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 445 | 41% helix, 18% strand | A0QWJ0 |
| C, D | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 447 | 41% helix, 18% strand | A0QWJ0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- FMT · Formic acid · additive · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.65 | 0.81 | 38 | FMT |
| 2 | 343 | 0.65 | 0.80 | 39 | EDO, FMT |
| 3 | 335 | 0.64 | 0.80 | 39 | FMT |
| 4 | 321 | 0.64 | 0.80 | 34 | FMT |
| 5 | 136 | 0.40 | 0.74 | 19 | FMT |
Interfaces
3 interfaces between chains.
- A–B · 4796 Ų buried · 102 hydrogen bonds · protein-protein
- C–D · 4790 Ų buried · 100 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3OKS · Crystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis · 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 A0QWJ0
- Elsewhere: RCSB PDB 3OKS · PDBe 3OKS · UniProt A0QWJ0
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