MolNFT v1 · #154213 · protein + DNA
Solution structure of APOBEC3G-CD2 with ssdna, product B
6K3K · DNA dc->du-editing enzyme apobec-3G: “Solution structure of APOBEC3G-CD2 with ssdna, product B”. Solution nmr, 1 ligand (ZN), 4 pockets (best druggability 0.73). MolNFT v1 #154213 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6K3K
- Type
- protein + DNA
- Length
- 198 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3G; DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3')
- EC
- 3.5.4.-
- UniProt
- Q9HC16
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.73
Structure
solution nmr · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 188 | 40% helix, 17% strand | Q9HC16 |
| B | DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.73 | 0.88 | 31 | empty |
| 2 | 94 | 0.58 | 0.86 | 23 | empty |
| 3 | 91 | 0.50 | 0.83 | 20 | empty |
| 4 | 50 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6K3K · Solution structure of APOBEC3G-CD2 with ssDNA, Product B · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HC16 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3G (Q9HC16) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 Q9HC16
- Elsewhere: RCSB PDB 6K3K · PDBe 6K3K · UniProt Q9HC16
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