Research workbench
The crystal structure of ASFVAP:AG
Analyse The crystal structure of ASFVAP:AG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KHY
- Type
- protein + DNA
- Length
- 1,294 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ap endonuclease; DNA(CCTCGTCGGGGACGCTG); DNA(GCAGCGTCACCGACGAGG)…
- EC
- 3.1.21.-
- UniProt
- P0C9C6
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable ap endonuclease (EC 3.1.21.-) | protein | 299 | 43% helix, 15% strand | P0C9C6 |
| E | DNA(CCTCGTCGGGGACGCTG) | dna | 17 | — | — |
| F | DNA(GCAGCGTCACCGACGAGG) | dna | 16 | — | — |
| G | DNA(CCTCGTCGGGGACGCT) | dna | 16 | — | — |
| H | DNA(AGCGTCACCGACGAGG) | dna | 16 | — | — |
| I | DNA(CCTCGTCGGGGACGC) | dna | 16 | — | — |
| J | DNA (agcgtcaccgacgaggc) | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, F, B, G, H, C, E, D, I, J
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, F, B, G, H, C, E, D, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.77 | 0.81 | 88 | MES |
| 2 | 159 | 0.69 | 0.89 | 30 | empty |
| 3 | 61 | 0.68 | 0.96 | 24 | empty |
| 4 | 206 | 0.54 | 0.79 | 43 | MES |
| 5 | 158 | 0.53 | 0.80 | 28 | MES |
Interfaces
16 interfaces between chains.
- I–J · 1834 Ų buried · 640 hydrogen bonds · nucleic-nucleic
- G–H · 1832 Ų buried · 652 hydrogen bonds · nucleic-nucleic
- E–F · 725 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–E · 534 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–F · 417 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6KHY · The crystal structure of AsfvAP:AG · 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 P0C9C6
- Elsewhere: RCSB PDB 6KHY · PDBe 6KHY · UniProt P0C9C6
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