Research workbench
Crystal structure of human 5' exonuclease appollo in complex with 5'DAMP
Analyse Crystal structure of human 5' exonuclease appollo in complex with 5'DAMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A1F
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5' exonuclease apollo
- EC
- 3.1.-.-
- UniProt
- Q9H816
- Ligands
- D5M, FE, NI
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5' exonuclease apollo (EC 3.1.-.-) | protein | 329 | 27% helix, 22% strand | Q9H816 |
| L | 5' exonuclease apollo (EC 3.1.-.-) | protein | 335 | 27% helix, 21% strand | Q9H816 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 4 copies · chains A, L
- FE · Fe (III) ion · metal · 2 copies · chains A, L
- NI · Nickel (II) ion · metal · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.77 | 0.79 | 100 | D5M |
| 2 | 196 | 0.50 | 0.77 | 32 | D5M |
| 3 | 87 | 0.44 | 0.80 | 19 | empty |
| 4 | 106 | 0.40 | 0.76 | 24 | empty |
| 5 | 117 | 0.40 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–L · 690 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7A1F · Crystal structure of human 5' exonuclease Appollo in complex with 5'dAMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H816 · AlphaFold monomer V2.0 prediction for 5' exonuclease apollo (Q9H816) · a predicted model of the same protein · 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 Q9H816
- Elsewhere: RCSB PDB 7A1F · PDBe 7A1F · UniProt Q9H816
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