MolNFT v1 · #116573 · protein
HIV-1 rev ntd dimers with variable crossing angles
5DHX · Anti-rev antibody Fab single-chain variable fragment, light…: “HIV-1 rev ntd dimers with variable crossing angles”. X-ray diffraction, 3 pockets (best druggability 0.41). MolNFT v1 #116573 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DHX
- Type
- protein
- Length
- 580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-rev antibody Fab single-chain variable fragment, light CHAIN,ANTI-rev antibody Fab…
- UniProt
- P69718
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Anti-rev antibody Fab single-chain variable fragment, light CHAIN,ANTI-rev antibody Fab single-chain variable fragment, heavy chain | protein | 231 | 3% helix, 50% strand | — |
| C, M | Protein rev | protein | 61 | 70% helix, 0% strand | P69718 |
| L | Anti-rev antibody Fab single-chain variable fragment, light CHAIN,ANTI-rev antibody Fab single-chain variable fragment, heavy chain | protein | 227 | 3% helix, 51% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.41 | 0.75 | 29 | empty |
| 2 | 158 | 0.41 | 0.74 | 17 | empty |
| 3 | 129 | 0.40 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 758 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 756 Ų buried · 18 hydrogen bonds · protein-protein
- B–L · 91 Ų buried · 0 hydrogen bonds · protein-protein
- B–M · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5DHX · HIV-1 Rev NTD dimers with variable crossing angles · the same entry in another collection · chain M against M, 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 P69718
- Elsewhere: RCSB PDB 5DHX · PDBe 5DHX · UniProt P69718
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