MolNFT v1 · #169783 · protein
Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from legionella pneumophila in complex with NAD
6XMY: “Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from legionella pneumophila in complex with…”. X-ray diffraction, 4 ligands (NAD, ZN, SO4), 5 pockets (best druggability 0.58). MolNFT v1 #169783 on GenesisL1: 3D…
- PDB
- 6XMY
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxythreonine-4-phosphate dehydrogenase
- EC
- 1.1.1.262
- UniProt
- Q3V872
- Ligands
- NAD, ZN, SO4, PO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262) | protein | 325 | 41% helix, 17% strand | Q3V872 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.58 | 0.84 | 25 | SO4, ZN |
| 2 | 70 | 0.49 | 0.84 | 17 | EDO |
| 3 | 117 | 0.42 | 0.76 | 17 | empty |
| 4 | 63 | 0.38 | 0.79 | 17 | EDO |
| 5 | 63 | 0.37 | 0.78 | 17 | empty |
Compared structures
- 6XMY · Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella… · 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 Q3V872
- Elsewhere: RCSB PDB 6XMY · PDBe 6XMY · UniProt Q3V872
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