MolNFT v1 · #110589 · protein
Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain
4Y1D: “Cyclic hexapeptide CYC[NDPOPPKID] in complex with HIV-1 integrase core domain”. X-ray diffraction, 3 ligands (CD, SO4, CL), 3 pockets (best druggability 0.63). MolNFT v1 #110589 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4Y1D
- Type
- protein
- Length
- 289 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Cyclic hexapeptide CYC[NDPOPPKID]
- UniProt
- F2WR39
- Ligands
- CD, SO4, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 141 | 51% helix, 21% strand | F2WR39 |
| B | Integrase | protein | 142 | 48% helix, 24% strand | F2WR39 |
| D | Cyclic hexapeptide CYC[NDPOPPKID] | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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 | 201 | 0.63 | 0.83 | 29 | empty |
| 2 | 107 | 0.49 | 0.80 | 22 | empty |
| 3 | 109 | 0.46 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1521 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 261 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 210 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified, 1 d-amino (nonstandard, D-amino acid).
Compared structures
- 4Y1D · 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 F2WR39
- Elsewhere: RCSB PDB 4Y1D · PDBe 4Y1D · UniProt F2WR39
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