Research workbench
Crystal structure of HIV-1 rev (residues 1-93)-RNA aptamer complex
Analyse Crystal structure of HIV-1 rev (residues 1-93)-RNA aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CF2
- Type
- protein + RNA
- Length
- 318 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-rev antibody, heavy chain; Anti-rev antibody, light chain; Protein rev; RNA (35-mer)
- UniProt
- Q76PP8
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-rev antibody, heavy chain | protein | 116 | 3% helix, 53% strand | — |
| B | Anti-rev antibody, light chain | protein | 110 | 0% helix, 47% strand | — |
| F | Protein rev | protein | 57 | 75% helix, 0% strand | Q76PP8 |
| G | RNA (35-mer) | rna | 35 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.53 | 0.76 | 21 | empty |
| 2 | 135 | 0.41 | 0.75 | 16 | empty |
| 3 | 100 | 0.39 | 0.77 | 14 | empty |
| 4 | 61 | 0.35 | 0.77 | 14 | empty |
| 5 | 59 | 0.26 | 0.73 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 931 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 854 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–F · 386 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 380 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 14 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6CF2 · Crystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex · the same entry in another collection · chain B against B, 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 Q76PP8
- Elsewhere: RCSB PDB 6CF2 · PDBe 6CF2 · UniProt Q76PP8
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