MolNFT v1 · #143849 · protein + RNA
Crystal structure of human APOBEC3H/RNA complex
6BBO: “Crystal structure of human APOBEC3H/RNA complex”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.72). MolNFT v1 #143849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BBO
- Type
- protein + RNA
- Length
- 802 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APOBEC3H; RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3'); RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')…
- UniProt
- B7TQM6, X5DSL3
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | APOBEC3H | protein | 180 | 38% helix, 21% strand | B7TQM6 |
| B, F | RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 8 | — | — |
| C, G | RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 8 | — | — |
| D, H | Mcherry fluorescent protein | protein | 205 | 5% helix, 57% strand | X5DSL3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.72 | 0.81 | 35 | empty |
| 2 | 323 | 0.72 | 0.84 | 42 | GOL |
| 3 | 338 | 0.71 | 0.84 | 48 | GOL |
| 4 | 441 | 0.71 | 0.82 | 35 | empty |
| 5 | 247 | 0.64 | 0.82 | 30 | empty |
Interfaces
11 interfaces between chains.
- A–E · 818 Ų buried · 6 hydrogen bonds · protein-protein
- E–H · 619 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 618 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–F · 542 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6BBO · Crystal structure of human APOBEC3H/RNA complex · 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 B7TQM6
- Every structure of UniProt X5DSL3
- Elsewhere: RCSB PDB 6BBO · PDBe 6BBO · UniProt B7TQM6 · UniProt X5DSL3
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