MolNFT v1 · #117818 · protein + DNA
Crystal structure of the rous sarcoma virus intasome
5EJK · Gag-pro-pol polyprotein: “Crystal structure of the rous sarcoma virus intasome”. X-ray diffraction, 2 ligands (W, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #117818 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EJK
- Type
- protein + DNA
- Length
- 2,216 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pro-pol polyprotein; Rsv integrase; DNA (5'…
- EC
- 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
- UniProt
- P03354
- Ligands
- W, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 13 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 269 | 37% helix, 22% strand | P03354 |
| B | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 253 | 40% helix, 23% strand | P03354 |
| C | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 256 | 37% helix, 22% strand | P03354 |
| D | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 250 | 39% helix, 21% strand | P03354 |
| F | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 254 | 38% helix, 22% strand | P03354 |
| G | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 250 | 38% helix, 22% strand | P03354 |
| H | Gag-pro-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 263 | 37% helix, 21% strand | P03354 |
| I | Rsv integrase | dna | 42 | — | — |
| J | DNA (5'- D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)- 3') | dna | 22 | — | — |
| K, N | DNA (5'-D(*CP*TP*TP*CP*TP*CP*TP*C)-3') | dna | 8 | — | — |
| L | Rsv integrase | dna | 38 | — | — |
| M | DNA (5'- D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)- 3') | dna | 18 | — | — |
| k, n | DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- W · Tungsten ion · metal · 36 copies · chains A, B, F
- ZN · Zinc ion · metal · 8 copies · chains A, E, B, C, D, F, G, H
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 | 787 | 0.83 | 0.87 | 82 | empty |
| 2 | 761 | 0.83 | 0.86 | 69 | empty |
| 3 | 779 | 0.81 | 0.84 | 67 | empty |
| 4 | 172 | 0.78 | 0.95 | 30 | empty |
| 5 | 511 | 0.78 | 0.85 | 56 | empty |
Interfaces
45 interfaces between chains.
- E–F · 1793 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1747 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1617 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1615 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1122 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 88 modified (engineered).
Compared structures
- 5EJK · Crystal structure of the Rous sarcoma virus intasome · 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 P03354
- Elsewhere: RCSB PDB 5EJK · PDBe 5EJK · UniProt P03354
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