MolNFT v1 · #46251 · protein
The APOBEC2 crystal structure and functional implications for aid
2NYT · Probable C->U-editing enzyme apobec-2: “The APOBEC2 crystal structure and functional implications for aid”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.77). MolNFT v1 #46251 on GenesisL1: 3D structure, binding…
- PDB
- 2NYT
- Type
- protein
- Length
- 739 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable C->U-editing enzyme apobec-2
- EC
- 3.5.4.-
- UniProt
- Q9Y235
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable C->U-editing enzyme apobec-2 (EC 3.5.4.-) | protein | 185 | 37% helix, 25% strand | Q9Y235 |
| B | Probable C->U-editing enzyme apobec-2 (EC 3.5.4.-) | protein | 190 | 36% helix, 29% strand | Q9Y235 |
| C | Probable C->U-editing enzyme apobec-2 (EC 3.5.4.-) | protein | 185 | 36% helix, 25% strand | Q9Y235 |
| D | Probable C->U-editing enzyme apobec-2 (EC 3.5.4.-) | protein | 179 | 38% helix, 28% strand | Q9Y235 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.77 | 0.96 | 27 | empty |
| 2 | 90 | 0.76 | 0.98 | 22 | empty |
| 3 | 258 | 0.62 | 0.80 | 29 | empty |
| 4 | 293 | 0.61 | 0.79 | 35 | empty |
| 5 | 102 | 0.52 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1224 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 956 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 725 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2NYT · The APOBEC2 Crystal Structure and Functional Implications for AID · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y235 · AlphaFold monomer V2.0 prediction for C->U-editing enzyme apobec-2 (Q9Y235) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 Q9Y235
- Elsewhere: RCSB PDB 2NYT · PDBe 2NYT · UniProt Q9Y235
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