Research workbench
Amine transaminase crystal structure from an uncultivated pseudomonas species in the pmp-bound form
Analyse Amine transaminase crystal structure from an uncultivated pseudomonas species… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHA
- Type
- protein
- Length
- 1,786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omega transaminase
- EC
- 2.6.1.18
- Ligands
- PMP
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Omega transaminase (EC 2.6.1.18) | protein | 447 | 42% helix, 20% strand | — |
| B, D | Omega transaminase (EC 2.6.1.18) | protein | 446 | 41% helix, 20% strand | — |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.87 | 0.89 | 147 | empty |
| 2 | 451 | 0.84 | 0.92 | 56 | empty |
| 3 | 1014 | 0.79 | 0.81 | 98 | PMP |
| 4 | 982 | 0.78 | 0.80 | 98 | PMP |
| 5 | 125 | 0.77 | 0.96 | 32 | PMP |
Interfaces
6 interfaces between chains.
- B–D · 5498 Ų buried · 90 hydrogen bonds · protein-protein
- A–C · 5492 Ų buried · 92 hydrogen bonds · protein-protein
- A–B · 954 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 921 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LHA · 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 5LHA · PDBe 5LHA
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