Research workbench
Structure of an ap endonuclease from archaeoglobus fulgidus
Analyse Structure of an ap endonuclease from archaeoglobus fulgidus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VOA
- Type
- protein + DNA
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease III; 5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3'…
- EC
- 4.2.99.18
- UniProt
- O29675
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exodeoxyribonuclease III (EC 4.2.99.18) | protein | 257 | 29% helix, 28% strand | O29675 |
| C | 5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3' | dna | 10 | — | — |
| D | 5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3' | dna | 10 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.71 | 0.82 | 52 | empty |
| 2 | 133 | 0.58 | 0.84 | 31 | empty |
| 3 | 125 | 0.48 | 0.80 | 21 | empty |
| 4 | 278 | 0.46 | 0.72 | 41 | empty |
Interfaces
5 interfaces between chains.
- C–D · 474 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–C · 455 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 409 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 238 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 206 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2VOA · Structure of an AP Endonuclease from Archaeoglobus fulgidus · 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 O29675
- Elsewhere: RCSB PDB 2VOA · PDBe 2VOA · UniProt O29675
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