MolNFT v1 · #97737 · protein
The crystal structure of apo human HDHD4 from se-mad
4KNV · N-acylneuraminate-9-phosphatase: “The crystal structure of apo human HDHD4 from se-mad”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.60). MolNFT v1 #97737 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KNV
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylneuraminate-9-phosphatase
- EC
- 3.1.3.29
- UniProt
- Q8TBE9
- Ligands
- MG, PO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acylneuraminate-9-phosphatase (EC 3.1.3.29) | protein | 241 | 53% helix, 12% strand | Q8TBE9 |
| B | N-acylneuraminate-9-phosphatase (EC 3.1.3.29) | protein | 234 | 54% helix, 12% strand | Q8TBE9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.60 | 0.78 | 30 | empty |
| 2 | 401 | 0.59 | 0.76 | 43 | PO4, MG |
| 3 | 229 | 0.51 | 0.76 | 26 | empty |
| 4 | 182 | 0.45 | 0.75 | 26 | PO4, MG |
| 5 | 72 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
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 Q8TBE9
- Elsewhere: RCSB PDB 4KNV · PDBe 4KNV · UniProt Q8TBE9
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