Research workbench
Human foamy virus integrase - catalytic core. magnesium- bound structure.
Analyse Human foamy virus integrase - catalytic core. magnesium- bound structure. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X6S
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- UniProt
- P14350
- Ligands
- MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 188 | 39% helix, 16% strand | P14350 |
| B | Integrase | protein | 184 | 41% helix, 17% strand | P14350 |
| C | Integrase | protein | 176 | 40% helix, 18% strand | P14350 |
| D | Integrase | protein | 175 | 41% helix, 18% strand | P14350 |
| E | Integrase | protein | 182 | 41% helix, 16% strand | P14350 |
| F | Integrase | protein | 181 | 40% helix, 17% strand | P14350 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.98 | 20 | empty |
| 2 | 71 | 0.74 | 0.97 | 21 | empty |
| 3 | 68 | 0.73 | 0.97 | 24 | empty |
| 4 | 148 | 0.71 | 0.90 | 34 | empty |
| 5 | 614 | 0.71 | 0.79 | 76 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1634 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1571 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 311 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2X6S · Human foamy virus integrase - catalytic core. Magnesium-bound structure. · 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 P14350
- Elsewhere: RCSB PDB 2X6S · PDBe 2X6S · UniProt P14350
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