MolNFT v1 · #39417 · protein
Crystal structure of a putative pyridoxamine 5'-phosphate oxidase (LDB0262) from lactobacillus delbrueckii subsp. at 1.60 a resolution
2HTD · Predicted flavin-nucleotide-binding protein from COG3576…: “Crystal structure of a putative pyridoxamine 5'-phosphate oxidase (LDB0262) from lactobacillus delbrueckii…”. X-ray diffraction, 2 ligands (SO4, CL), 2 pockets (best…
- PDB
- 2HTD
- Type
- protein
- Length
- 245 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to…
- UniProt
- Q1GBW8
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase | protein | 121 | 19% helix, 44% strand | Q1GBW8 |
| B | Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase | protein | 124 | 19% helix, 43% strand | Q1GBW8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.68 | 0.89 | 28 | SO4 |
| 2 | 172 | 0.44 | 0.75 | 27 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2HTD · Crystal structure of a putative pyridoxamine 5'-phosphate oxidase (LDB0262) from… · 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
- Every structure of UniProt Q1GBW8
- Elsewhere: RCSB PDB 2HTD · PDBe 2HTD · UniProt Q1GBW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.