Research workbench
Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain
Analyse Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y1C
- Type
- protein
- Length
- 292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Cyclic hexapeptide CYC[NDPOPPKID]
- UniProt
- Q76353
- Ligands
- CD, SO4
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 145 | 46% helix, 24% strand | Q76353 |
| B | Integrase | protein | 141 | 49% helix, 23% strand | Q76353 |
| C | Cyclic hexapeptide CYC[NDPOPPKID] | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 119 | 0.50 | 0.80 | 18 | empty |
| 2 | 96 | 0.44 | 0.79 | 20 | empty |
| 3 | 90 | 0.43 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1542 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 d-amino, 1 modified (D-amino acid, nonstandard).
Compared structures
- 4Y1C · Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain · 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 Q76353
- Elsewhere: RCSB PDB 4Y1C · PDBe 4Y1C · UniProt Q76353
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