MolNFT v1 · #116574 · protein
HIV-1 rev ntd dimers with variable crossing angles
5DHY · Anti-rev antibody Fab single-chain variable fragment, heavy…: “HIV-1 rev ntd dimers with variable crossing angles”. X-ray diffraction, 6 pockets (best druggability 0.60). MolNFT v1 #116574 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DHY
- Type
- protein
- Length
- 576 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-rev antibody Fab single-chain variable fragment, heavy chain; Anti-rev antibody Fab…
- UniProt
- Q76PP8
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Anti-rev antibody Fab single-chain variable fragment, heavy chain | protein | 117 | 3% helix, 52% strand | — |
| B, L | Anti-rev antibody Fab single-chain variable fragment, light chain | protein | 110 | 3% helix, 51% strand | — |
| C, M | Protein rev | protein | 61 | 79% helix, 0% strand | Q76PP8 |
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 | 369 | 0.60 | 0.77 | 37 | empty |
| 2 | 378 | 0.58 | 0.75 | 34 | empty |
| 3 | 69 | 0.34 | 0.76 | 16 | empty |
| 4 | 73 | 0.32 | 0.74 | 19 | empty |
| 5 | 62 | 0.26 | 0.72 | 17 | empty |
Interfaces
10 interfaces between chains.
- H–L · 918 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 8 hydrogen bonds · protein-protein
- H–M · 437 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 405 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5DHY · HIV-1 Rev NTD dimers with variable crossing angles · 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 Q76PP8
- Elsewhere: RCSB PDB 5DHY · PDBe 5DHY · UniProt Q76PP8
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