MolNFT v1 · #125714 · protein
Amine transaminase crystal structure from an uncultivated pseudomonas species in the plp-bound (internal aldimine) form
5LH9 · Omega transaminase: “Amine transaminase crystal structure from an uncultivated pseudomonas species in the plp-bound (internal…”. X-ray diffraction, 1 ligand (PLP), 12 pockets (best druggability 0.87). MolNFT v1 #125714 on GenesisL1…
- PDB
- 5LH9
- Type
- protein
- Length
- 1,787 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omega transaminase
- EC
- 2.6.1.18
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Omega transaminase (EC 2.6.1.18) | protein | 444 | 41% helix, 20% strand | — |
| B, C | Omega transaminase (EC 2.6.1.18) | protein | 447 | 41% helix, 20% strand | — |
| D | Omega transaminase (EC 2.6.1.18) | protein | 449 | 41% helix, 19% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.87 | 0.88 | 142 | empty |
| 2 | 251 | 0.81 | 0.94 | 45 | empty |
| 3 | 924 | 0.77 | 0.80 | 70 | empty |
| 4 | 103 | 0.77 | 0.97 | 35 | PLP |
| 5 | 96 | 0.77 | 0.97 | 35 | PLP |
Interfaces
6 interfaces between chains.
- B–C · 5438 Ų buried · 88 hydrogen bonds · protein-protein
- A–D · 5391 Ų buried · 90 hydrogen bonds · protein-protein
- A–C · 1054 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 968 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LH9 · Amine transaminase crystal structure from an uncultivated Pseudomonas species in the… · 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
- Elsewhere: RCSB PDB 5LH9 · PDBe 5LH9
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