Research workbench
Cyclic hexapeptide pkzdnv in complex with HIV-1 integrase
Analyse Cyclic hexapeptide pkzdnv in complex with HIV-1 integrase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WNH
- Type
- protein
- Length
- 283 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein; PK(NLE)DN(DVA) peptide
- UniProt
- P12497
- Ligands
- CD, SO4, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-pol polyprotein | protein | 137 | 50% helix, 20% strand | P12497 |
| B | Gag-pol polyprotein | protein | 134 | 51% helix, 21% strand | P12497 |
| C, D | PK(NLE)DN(DVA) peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.52 | 0.77 | 24 | empty |
| 2 | 96 | 0.45 | 0.79 | 25 | empty |
| 3 | 63 | 0.37 | 0.79 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1538 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 d-amino, 2 modified (D-amino acid, nonstandard).
Compared structures
- 3WNH · Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase · 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 P12497
- Elsewhere: RCSB PDB 3WNH · PDBe 3WNH · UniProt P12497
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