Research workbench
Pfv intasome - nucleosome strand transfer complex
Analyse Pfv intasome - nucleosome strand transfer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RNY
- Type
- protein + DNA
- Length
- 2,100 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; Integrase…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-
- UniProt
- P84243, P62805, P0C0S8, P62807, P14350
- Ligands
- MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 12 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.3 | protein | 97 | 64% helix, 3% strand | P84243 |
| B, F | Histone H4 | protein | 83 | 49% helix, 5% strand | P62805 |
| C, G | Histone H2A type 1 | protein | 110 | 38% helix, 5% strand | P0C0S8 |
| D, H | Histone H2B type 1-C/E/F/G/I | protein | 94 | 65% helix, 4% strand | P62807 |
| K, O | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 338 | 24% helix, 17% strand | P14350 |
| L | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 141 | 37% helix, 12% strand | P14350 |
| P | Integrase (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-, 2.7.7.-, 3.1.-.-) | protein | 157 | 34% helix, 15% strand | P14350 |
| I | DNA (128-mer) | dna | 128 | — | — |
| U | DNA (108-mer) | dna | 108 | — | — |
| T | DNA (33-mer) | dna | 33 | — | — |
| J | DNA (53-mer) | dna | 53 | — | — |
| Q, M | DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains K, U, J, O, I, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.80 | 0.84 | 78 | empty |
| 2 | 1039 | 0.80 | 0.81 | 138 | empty |
| 3 | 888 | 0.75 | 0.79 | 64 | empty |
| 4 | 256 | 0.73 | 0.88 | 34 | empty |
| 5 | 79 | 0.72 | 0.96 | 24 | empty |
Interfaces
66 interfaces between chains.
- I–U · 4704 Ų buried · 468 hydrogen bonds · nucleic-nucleic
- A–B · 2792 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2766 Ų buried · 18 hydrogen bonds · protein-protein
- K–O · 2641 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6RNY · PFV intasome - nucleosome strand transfer complex · the same entry in another collection · chain M against M, 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 P84243
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Every structure of UniProt P14350
- Elsewhere: RCSB PDB 6RNY · PDBe 6RNY · UniProt P84243 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt P14350
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