Research workbench
Structure of plp internal aldimine form of sphingopyxis sp. MTA144 fumi protein
Analyse Structure of plp internal aldimine form of sphingopyxis sp. MTA144 fumi protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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