Research workbench
The crystal structure of ASFVAP:DF commplex
Analyse The crystal structure of ASFVAP:DF commplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KI3
- Type
- protein + DNA
- Length
- 666 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ap endonuclease; DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3'); DNA…
- EC
- 3.1.21.-
- UniProt
- P0C9C6
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ap endonuclease (EC 3.1.21.-) | protein | 298 | 44% helix, 15% strand | P0C9C6 |
| C, F | DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3') | dna | 9 | — | — |
| D, G | DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*AP*G)-3') | dna | 8 | — | — |
| E, H | DNA (5'- D(*CP*CP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*CP*TP*G)-3') | dna | 17 | — | — |
| B | Probable ap endonuclease (EC 3.1.21.-) | protein | 300 | 44% helix, 15% strand | P0C9C6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, D, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.72 | 0.90 | 32 | empty |
| 2 | 336 | 0.70 | 0.84 | 32 | empty |
| 3 | 366 | 0.56 | 0.75 | 38 | empty |
| 4 | 364 | 0.55 | 0.74 | 31 | empty |
| 5 | 125 | 0.50 | 0.80 | 24 | empty |
Interfaces
13 interfaces between chains.
- A–E · 662 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–H · 606 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–G · 568 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 555 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 428 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 6KI3 · The crystal structure of AsfvAP:dF commplex · 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 6KI3 · PDBe 6KI3 · UniProt P0C9C6
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