Research workbench
Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A
Analyse Non-specific and specific interactions work cooperatively to promote cytidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3V
- Type
- protein + DNA
- Length
- 418 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3A; DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3')
- EC
- 3.5.4.38
- UniProt
- P31941
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.73
Structure
solution nmr · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA dc->du-editing enzyme apobec-3A (EC 3.5.4.38) | protein | 199 | 36% helix, 22% strand | P31941 |
| C, D | DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.73 | 0.80 | 55 | empty |
| 2 | 128 | 0.72 | 0.92 | 28 | empty |
| 3 | 552 | 0.71 | 0.79 | 54 | empty |
| 4 | 164 | 0.68 | 0.88 | 23 | empty |
| 5 | 82 | 0.66 | 0.91 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1478 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1123 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 813 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 7D3V · Non-specific and specific interactions work cooperatively to promote cytidine deamination… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.84
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 7D3V · PDBe 7D3V · UniProt P31941
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