Research workbench
Human ornithine aminotransferase complexed with the neurotoxin gabaculine
Analyse Human ornithine aminotransferase complexed with the neurotoxin gabaculine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GBN
- Type
- protein
- Length
- 1,206 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase
- EC
- 2.6.1.13
- UniProt
- P04181
- Ligands
- PLP, GBC, GAB
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ornithine aminotransferase (EC 2.6.1.13) | protein | 402 | 39% helix, 20% strand | P04181 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- GBC · Gabaculine · ligand · 2 copies · chains A, B, C
- GAB · 3-aminobenzoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.77 | 0.87 | 60 | GBC, PLP |
| 2 | 424 | 0.77 | 0.86 | 56 | GAB, PLP |
| 3 | 780 | 0.72 | 0.77 | 51 | empty |
| 4 | 586 | 0.66 | 0.76 | 62 | GBC, PLP |
| 5 | 50 | 0.43 | 0.84 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5258 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 595 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1GBN · Human ornithine aminotransferase complexed with the neurotoxin gabaculine · the same entry in another collection · chain A against A, TM-score 1.00
- P04181 · AlphaFold monomer V2.0 prediction for ornithine aminotransferase, mitochondrial (P04181) · a predicted model of the same protein · 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 P04181
- Elsewhere: RCSB PDB 1GBN · PDBe 1GBN · UniProt P04181
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.