Research workbench
Crystal structure of the pdxy protein from escherichia COLI
Analyse Crystal structure of the pdxy protein from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TD2
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine kinase
- EC
- 2.7.1.35
- UniProt
- P77150
- Ligands
- PXL, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyridoxamine kinase (EC 2.7.1.35) | protein | 287 | 42% helix, 18% strand | P77150 |
Ligands and binding sites
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.76 | 0.85 | 43 | SO4, PXL |
| 2 | 497 | 0.71 | 0.81 | 49 | PXL |
| 3 | 86 | 0.51 | 0.84 | 16 | empty |
| 4 | 73 | 0.45 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1803 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 P77150
- Elsewhere: RCSB PDB 1TD2 · PDBe 1TD2 · UniProt P77150
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