Research workbench
Crystal structure of the primate APOBEC3H dimer mediated by RNA duplex
Analyse Crystal structure of the primate APOBEC3H dimer mediated by RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z98
- Type
- protein + RNA
- Length
- 381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein B mRNA editing enzyme catalytic polypeptide- like protein 3H; RNA…
- UniProt
- B7T0U6
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Apolipoprotein B mRNA editing enzyme catalytic polypeptide- like protein 3H | protein | 182 | 41% helix, 20% strand | B7T0U6 |
| C | RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3') | rna | 9 | — | — |
| D | RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3') | rna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.71 | 0.82 | 34 | empty |
| 2 | 486 | 0.58 | 0.73 | 53 | empty |
| 3 | 58 | 0.45 | 0.83 | 18 | empty |
| 4 | 135 | 0.40 | 0.74 | 25 | empty |
| 5 | 91 | 0.40 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 562 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 343 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–D · 309 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 245 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Z98 · Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex · 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
- Every structure of UniProt B7T0U6
- Elsewhere: RCSB PDB 5Z98 · PDBe 5Z98 · UniProt B7T0U6
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