Research workbench
Crystal structure of 2-aminoethylphosphonate transaminase
Analyse Crystal structure of 2-aminoethylphosphonate transaminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M32
- Type
- protein
- Length
- 2,169 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-aminoethylphosphonate-pyruvate aminotransferase
- EC
- 2.6.1.37
- UniProt
- P96060
- Ligands
- PLP, POA, PO4
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | 2-aminoethylphosphonate-pyruvate aminotransferase (EC 2.6.1.37) | protein | 361 | 41% helix, 17% strand | P96060 |
| B, D, F | 2-aminoethylphosphonate-pyruvate aminotransferase (EC 2.6.1.37) | protein | 362 | 41% helix, 17% strand | P96060 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- POA · Phosphonoacetaldehyde · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.72 | 0.86 | 43 | PO4, PLP |
| 2 | 840 | 0.72 | 0.77 | 85 | empty |
| 3 | 315 | 0.72 | 0.85 | 41 | PLP, POA |
| 4 | 319 | 0.71 | 0.84 | 45 | PLP, POA |
| 5 | 292 | 0.71 | 0.85 | 47 | PO4, PLP |
Interfaces
8 interfaces between chains.
- A–B · 2369 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2327 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2248 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 473 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 171 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 1M32 · Crystal Structure of 2-aminoethylphosphonate Transaminase · the same entry in another collection · chain F against F, TM-score 1.00
- P96060 · AlphaFold monomer V2.0 prediction for 2-aminoethylphosphonate-- pyruvate transaminase… · a predicted model of the same protein · chain B 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 P96060
- Elsewhere: RCSB PDB 1M32 · PDBe 1M32 · UniProt P96060
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