MolNFT v1 · #66410 · protein
Closed tetramer of visna virus integrase (residues 1-219) in complex with ledgf ibd
3HPH: “Closed tetramer of visna virus integrase (residues 1-219) in complex with ledgf ibd”. X-ray diffraction, 2 ligands (ZN, PO4), 14 pockets (best druggability 0.81). MolNFT v1 #66410 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HPH
- Type
- protein
- Length
- 1,086 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; PC4 and SFRS1-interacting protein
- UniProt
- P35956, O75475
- Ligands
- ZN, PO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 194 | 57% helix, 16% strand | P35956 |
| B | Integrase | protein | 200 | 54% helix, 17% strand | P35956 |
| C | Integrase | protein | 202 | 53% helix, 17% strand | P35956 |
| D | Integrase | protein | 196 | 56% helix, 16% strand | P35956 |
| E | PC4 and SFRS1-interacting protein | protein | 89 | 81% helix, 0% strand | O75475 |
| F | PC4 and SFRS1-interacting protein | protein | 60 | 73% helix, 0% strand | O75475 |
| G | PC4 and SFRS1-interacting protein | protein | 54 | 78% helix, 0% strand | O75475 |
| H | PC4 and SFRS1-interacting protein | protein | 91 | 79% helix, 0% strand | O75475 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains B, E, H
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.81 | 0.84 | 66 | empty |
| 2 | 91 | 0.77 | 0.97 | 23 | GOL |
| 3 | 375 | 0.71 | 0.82 | 53 | GOL |
| 4 | 409 | 0.67 | 0.80 | 37 | empty |
| 5 | 373 | 0.66 | 0.80 | 35 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1538 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1526 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1522 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 420 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3HPH · Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD · the same entry in another collection · chain H against H, TM-score 1.00
- O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P35956
- Every structure of UniProt O75475
- Elsewhere: RCSB PDB 3HPH · PDBe 3HPH · UniProt P35956 · UniProt O75475
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