MolNFT v1 · #137939 · protein + RNA
Crystal structure of macaque APOBEC3H in complex with RNA
5W3V: “Crystal structure of macaque APOBEC3H in complex with RNA”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.80). MolNFT v1 #137939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W3V
- Type
- protein + RNA
- Length
- 775 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APOBEC3H; RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3'); RNA…
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APOBEC3H | protein | 186 | 43% helix, 21% strand | — |
| B | APOBEC3H | protein | 182 | 41% helix, 20% strand | — |
| C | APOBEC3H | protein | 184 | 42% helix, 21% strand | — |
| D | APOBEC3H | protein | 183 | 43% helix, 20% strand | — |
| E, H | RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3') | rna | 10 | — | — |
| F, G | RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3') | rna | 10 | — | — |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.80 | 0.82 | 93 | empty |
| 2 | 567 | 0.80 | 0.86 | 62 | empty |
| 3 | 71 | 0.70 | 0.96 | 16 | empty |
| 4 | 175 | 0.48 | 0.76 | 20 | empty |
| 5 | 88 | 0.44 | 0.79 | 19 | empty |
Interfaces
18 interfaces between chains.
- C–G · 660 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–F · 631 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–H · 583 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 571 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 499 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 5W3V · Crystal Structure of macaque APOBEC3H in complex with RNA · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5W3V · PDBe 5W3V
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