2X6N: Integrase
Human foamy virus integrase - catalytic core. Manganese-bound structure. Determined by X-ray diffraction at 2.06 Å resolution. Released 11 Aug 2010.
- Method
- X-ray diffraction
- Resolution
- 2.06 Å
- Organism
- HUMAN SPUMARETROVIRUS
- Chains
- 6
- Atoms
- 9,059
- Mol. weight
- 135.8 kDa
- Ligands
- MN
- Released
- 11 Aug 2010
Explore 2X6N in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2X6N contains 50 α-helices and 46 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 1 |
| β-strand | 136 | 1 | 2 |
| β-strand | 139 | 1 | 2 |
| β-strand | 141-147 | 7 | 1 |
| β-strand | 153-158 | 6 | 1 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-184 | 4 | 1 |
| α-helix | 188-191 | 4 | |
| α-helix | 193-200 | 8 | |
| α-helix | 204 | 1 | |
| β-strand | 205-208 | 4 | 1 |
| α-helix | 219-236 | 18 | |
| α-helix | 242-254 | 13 | |
| α-helix | 265-270 | 6 | |
| α-helix | 275-276 | 2 | |
| α-helix | 289-301 | 13 | |
Chain B: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 3 |
| β-strand | 136 | 1 | 4 |
| β-strand | 139 | 1 | 4 |
| β-strand | 141-147 | 7 | 3 |
| β-strand | 153-158 | 6 | 3 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-184 | 4 | 3 |
| α-helix | 188-191 | 4 | |
| β-strand | 192 | 1 | 5 |
| α-helix | 193-202 | 10 | |
| α-helix | 204 | 1 | |
| β-strand | 205-208 | 4 | 3 |
| α-helix | 222-236 | 15 | |
| α-helix | 242-254 | 13 | |
| α-helix | 265-270 | 6 | |
| α-helix | 289-301 | 13 | |
Chain C: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 6 |
| β-strand | 136 | 1 | 7 |
| β-strand | 139 | 1 | 7 |
| β-strand | 141-147 | 7 | 6 |
| β-strand | 153-158 | 6 | 6 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-184 | 4 | 6 |
| α-helix | 188-191 | 4 | |
| α-helix | 193-202 | 10 | |
| α-helix | 204 | 1 | |
| β-strand | 205-208 | 4 | 6 |
| α-helix | 220-236 | 17 | |
| α-helix | 242-254 | 13 | |
| α-helix | 265-270 | 6 | |
| β-strand | 274 | 1 | 5 |
| α-helix | 289-299 | 11 | |
Chain D: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 8 |
| β-strand | 136 | 1 | 9 |
| β-strand | 139 | 1 | 9 |
| β-strand | 141-147 | 7 | 8 |
| β-strand | 153-158 | 6 | 8 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-183 | 3 | 8 |
| α-helix | 188-191 | 4 | |
| α-helix | 193-201 | 9 | |
| α-helix | 204 | 1 | |
| β-strand | 205-207 | 3 | 8 |
| α-helix | 221-237 | 17 | |
| α-helix | 242-254 | 13 | |
| β-strand | 258 | 1 | 10 |
| β-strand | 263 | 1 | 10 |
| α-helix | 265-270 | 6 | |
| α-helix | 275-276 | 2 | |
| α-helix | 289-301 | 13 | |
Chain E: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 11 |
| β-strand | 136 | 1 | 12 |
| β-strand | 139 | 1 | 12 |
| β-strand | 141-147 | 7 | 11 |
| β-strand | 153-158 | 6 | 11 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-184 | 4 | 11 |
| α-helix | 188-191 | 4 | |
| α-helix | 193-202 | 10 | |
| α-helix | 204 | 1 | |
| β-strand | 205-208 | 4 | 11 |
| α-helix | 221-236 | 16 | |
| α-helix | 242-254 | 13 | |
| α-helix | 265-270 | 6 | |
| α-helix | 289-300 | 12 | |
Chain F: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 124-130 | 7 | 13 |
| β-strand | 136 | 1 | 14 |
| β-strand | 139 | 1 | 14 |
| β-strand | 141-147 | 7 | 13 |
| β-strand | 153-158 | 6 | 13 |
| α-helix | 163-173 | 11 | |
| β-strand | 181-184 | 4 | 13 |
| α-helix | 188-191 | 4 | |
| α-helix | 193-201 | 9 | |
| α-helix | 204 | 1 | |
| β-strand | 205-208 | 4 | 13 |
| α-helix | 220-236 | 17 | |
| α-helix | 242-254 | 13 | |
| α-helix | 265-270 | 6 | |
| α-helix | 289-301 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Integrase | A, B, C, D, E, F | protein | 200 | HUMAN SPUMARETROVIRUS | P14350 |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>2X6N_1 INTEGRASE (chains A, B, C, D, E, F)
GPILRPDRPQKPFDKFFMDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKS
LNVLTSIAIPRVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSGSKVERKNSDMKR
LLTKLLVGRPTKWYDLLPVVQLAMNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTRE
EELSLLQEIRTSLYHPSTPP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MN | Manganese (II) ion | Mn | 6 |
Primary citation
Structural Studies of the Catalytic Core of the Primate Foamy Virus (Pfv-1) Integrase. Rety, S., Rezabkova, L., Dubanchet, B. et al. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 66:881. DOI 10.1107/S1744309110022852 · PubMed
Other PDB entries of the same protein (UniProt P14350), best resolution first:
- 2X78 2.0 Å, Human foamy virus integrase - catalytic core.
- 3OYM 2.02 Å, Crystal structure of the PFV N224H mutant intasome bound to manganese
- 3DLR 2.2 Å, Crystal structure of the catalytic core domain from PFV integrase
- 2X6S 2.29 Å, Human foamy virus integrase - catalytic core. Magnesium-bound structure.
- 2X74 2.34 Å, Human foamy virus integrase - catalytic core.
- 4BE2 2.38 Å, PFV intasome with inhibitor XZ-259
- 3S3M 2.49 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…
- 3S3N 2.49 Å, Crystal structure of the Prototype Foamy Virus (PFV) S217H mutant intasome in complex…
- 3OYF 2.51 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…
- 4BDY 2.52 Å, PFV intasome with inhibitor XZ-89
- 4E7I 2.53 Å, PFV intasome freeze-trapped prior to 3'-processing, Mn-bound form (UI-Mn)
- 3OYB 2.54 Å, Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium…
Browse structure collections
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