MolNFT v1 · #160219 · protein + DNA
Drosophila P element transposase strand transfer complex
6PE2 · Transposable element P transposase: “Drosophila P element transposase strand transfer complex”. Electron microscopy, 2 ligands (GTP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #160219 on GenesisL1: 3D structure, binding…
- PDB
- 6PE2
- Type
- protein + DNA
- Length
- 1,318 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposable element P transposase; DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3'); DNA…
- EC
- 2.7.7.-
- UniProt
- Q7M3K2
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Transposable element P transposase (EC 2.7.7.-) | protein | 456 | 49% helix, 13% strand | Q7M3K2 |
| B, H | Transposable element P transposase (EC 2.7.7.-) | protein | 118 | 58% helix, 3% strand | Q7M3K2 |
| C, I | DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3') | dna | 9 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
| E | DNA (56-mer) | dna | 56 | — | — |
| J | DNA (27-mer) | dna | 20 | — | — |
| K | DNA (56-mer) | dna | 49 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, K, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, K, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.83 | 0.88 | 64 | empty |
| 2 | 360 | 0.80 | 0.90 | 53 | empty |
| 3 | 420 | 0.78 | 0.87 | 43 | empty |
| 4 | 340 | 0.77 | 0.88 | 40 | GTP, MG |
| 5 | 210 | 0.76 | 0.92 | 33 | empty |
Interfaces
26 interfaces between chains.
- E–G · 1482 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–K · 1469 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–E · 1400 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- A–G · 1371 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 1136 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PE2 · Drosophila P element transposase strand transfer complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q7M3K2 · AlphaFold monomer V2.0 prediction for transposable element P transposase (Q7M3K2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q7M3K2
- Elsewhere: RCSB PDB 6PE2 · PDBe 6PE2 · UniProt Q7M3K2
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