Research workbench
Structure of GABA-transaminase A1R958 from arthrobacter aurescens in complex with plp
Analyse Structure of GABA-transaminase A1R958 from arthrobacter aurescens in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ATP
- Type
- protein
- Length
- 5,280 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-aminobutyrate transaminase
- EC
- 2.6.1.19
- UniProt
- A1R958
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 442 | 39% helix, 17% strand | A1R958 |
| B, E | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 442 | 39% helix, 18% strand | A1R958 |
| D, F, K | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 439 | 39% helix, 18% strand | A1R958 |
| G, H | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 440 | 39% helix, 18% strand | A1R958 |
| I | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 441 | 39% helix, 17% strand | A1R958 |
| J | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 438 | 39% helix, 18% strand | A1R958 |
| L | 4-aminobutyrate transaminase (EC 2.6.1.19) | protein | 436 | 39% helix, 18% strand | A1R958 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, L, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.86 | 0.87 | 131 | PLP |
| 2 | 898 | 0.84 | 0.86 | 68 | empty |
| 3 | 1024 | 0.84 | 0.85 | 71 | empty |
| 4 | 974 | 0.84 | 0.85 | 72 | empty |
| 5 | 989 | 0.83 | 0.84 | 70 | empty |
Interfaces
26 interfaces between chains.
- C–D · 4588 Ų buried · 76 hydrogen bonds · protein-protein
- I–L · 4585 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 4580 Ų buried · 77 hydrogen bonds · protein-protein
- J–K · 4571 Ų buried · 75 hydrogen bonds · protein-protein
- G–H · 4570 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4ATP · Structure of GABA-transaminase A1R958 from Arthrobacter aurescens in complex with PLP · the same entry in another collection · chain E against E, 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 A1R958
- Elsewhere: RCSB PDB 4ATP · PDBe 4ATP · UniProt A1R958
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