MolNFT v1 · #151046 · protein
Structure of plp internal aldimine form of sphingopyxis sp. MTA144 fumi protein
6HBV · Aminopentol aminotransferase: “Structure of plp internal aldimine form of sphingopyxis sp. MTA144 fumi protein”. X-ray diffraction, 3 ligands (PLP, PMP, MG), 8 pockets (best druggability 0.81). MolNFT v1 #151046 on GenesisL1: 3D…
- PDB
- 6HBV
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopentol aminotransferase
- EC
- 2.6.1.-
- UniProt
- D2D3B2
- Ligands
- PLP, PMP, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopentol aminotransferase (EC 2.6.1.-) | protein | 414 | 41% helix, 15% strand | D2D3B2 |
| B | Aminopentol aminotransferase (EC 2.6.1.-) | protein | 411 | 42% helix, 16% strand | D2D3B2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.81 | 0.96 | 42 | empty |
| 2 | 79 | 0.74 | 0.97 | 25 | empty |
| 3 | 498 | 0.74 | 0.82 | 69 | PLP, PMP |
| 4 | 480 | 0.72 | 0.81 | 68 | PLP, PMP |
| 5 | 66 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4391 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6HBV · Structure of PLP internal aldimine form of Sphingopyxis sp. MTA144 FumI protein · the same entry in another collection · chain A against A, TM-score 1.00
- D2D3B2 · AlphaFold monomer V2.0 prediction for aminopentol aminotransferase (D2D3B2) · 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 D2D3B2
- Elsewhere: RCSB PDB 6HBV · PDBe 6HBV · UniProt D2D3B2
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