Research workbench
Kpacka (pduw) with amppnp, ethylene glycol complex structure
Analyse Kpacka (pduw) with amppnp, ethylene glycol complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FJA
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable propionate kinase
- EC
- 2.7.2.15
- UniProt
- A0A0H3GUQ7
- Ligands
- ANP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable propionate kinase (EC 2.7.2.15) | protein | 395 | 43% helix, 21% strand | A0A0H3GUQ7 |
| B | Probable propionate kinase (EC 2.7.2.15) | protein | 322 | 41% helix, 17% strand | A0A0H3GUQ7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.84 | 0.92 | 57 | empty |
| 2 | 573 | 0.67 | 0.77 | 54 | EDO |
| 3 | 215 | 0.62 | 0.82 | 25 | empty |
| 4 | 401 | 0.61 | 0.76 | 44 | empty |
| 5 | 57 | 0.44 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3027 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7FJA · KpAckA (PduW) with AMPPNP, ethylene glycol complex structure · 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 A0A0H3GUQ7
- Elsewhere: RCSB PDB 7FJA · PDBe 7FJA · UniProt A0A0H3GUQ7
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