Research workbench
Crystal structure of a C. elegans AP4A hydrolase binary complex
Analyse Crystal structure of a C. elegans AP4A hydrolase binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KTG
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diadenosine tetraphosphate hydrolase
- EC
- 3.6.1.17
- UniProt
- Q9U2M7
- Ligands
- AMP, MG, PO4, OH
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diadenosine tetraphosphate hydrolase (EC 3.6.1.17) | protein | 137 | 29% helix, 44% strand | Q9U2M7 |
| B | Diadenosine tetraphosphate hydrolase (EC 3.6.1.17) | protein | 132 | 30% helix, 38% strand | Q9U2M7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 9 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.57 | 0.76 | 40 | empty |
| 2 | 175 | 0.49 | 0.77 | 32 | PO4, MG |
| 3 | 129 | 0.44 | 0.77 | 26 | PO4, MG, AMP |
| 4 | 95 | 0.35 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 257 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1KTG · Crystal Structure of a C. elegans Ap4A Hydrolase Binary Complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U2M7 · AlphaFold monomer V2.0 prediction for BIS(5'-nucleosyl)-tetraphosphatase [asymmetrical]… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9U2M7
- Elsewhere: RCSB PDB 1KTG · PDBe 1KTG · UniProt Q9U2M7
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