Research workbench
Crystal structure of human APOBEC3A complexed with ssdna
Analyse Crystal structure of human APOBEC3A complexed with ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SWW
- Type
- protein + DNA
- Length
- 760 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3A; DNA 15-mer
- EC
- 3.5.4.-
- UniProt
- P31941
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA dc->du-editing enzyme apobec-3A (EC 3.5.4.-) | protein | 183 | 35% helix, 25% strand | P31941 |
| C | DNA dc->du-editing enzyme apobec-3A (EC 3.5.4.-) | protein | 185 | 36% helix, 24% strand | P31941 |
| D | DNA dc->du-editing enzyme apobec-3A (EC 3.5.4.-) | protein | 187 | 35% helix, 23% strand | P31941 |
| E, F | DNA 15-mer | dna | 5 | — | — |
| G, H | DNA 15-mer | dna | 6 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, E, B, F, C, G, D, H
- GOL · Glycerol · additive · 4 copies · chains B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.68 | 0.81 | 38 | empty |
| 2 | 288 | 0.56 | 0.76 | 32 | empty |
| 3 | 159 | 0.50 | 0.78 | 25 | empty |
| 4 | 92 | 0.48 | 0.82 | 16 | empty |
| 5 | 61 | 0.31 | 0.75 | 15 | empty |
Interfaces
10 interfaces between chains.
- B–F · 725 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 708 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–H · 689 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–G · 682 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 583 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5SWW · Crystal Structure of Human APOBEC3A complexed with ssDNA · the same entry in another collection · chain H against H, TM-score 1.00
- P31941 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3A (P31941) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P31941
- Elsewhere: RCSB PDB 5SWW · PDBe 5SWW · UniProt P31941
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