MolNFT v1 · #159921 · protein + DNA
Drosophila P element transposase strand transfer complex
6P5A · Transposable element P transposase: “Drosophila P element transposase strand transfer complex”. Electron microscopy, 2 ligands (GTP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #159921 on GenesisL1: 3D structure, binding…
- PDB
- 6P5A
- Type
- protein + DNA
- Length
- 1,256 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 0.84
Structure
electron microscopy · 5 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Transposable element P transposase (EC 2.7.7.-) | protein | 442 | 48% 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, J | DNA (5'-D(P*AP*GP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*CP*GP*G)- 3') | dna | 15 | — | — |
| E, K | DNA (44-mer) | dna | 44 | — | — |
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, E, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.84 | 0.85 | 77 | empty |
| 2 | 670 | 0.84 | 0.88 | 72 | empty |
| 3 | 1136 | 0.82 | 0.84 | 98 | empty |
| 4 | 342 | 0.77 | 0.88 | 44 | GTP, MG |
| 5 | 447 | 0.76 | 0.85 | 46 | GTP, MG |
Interfaces
26 interfaces between chains.
- A–K · 1532 Ų buried · 31 hydrogen bonds · protein-nucleic
- E–G · 1527 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–G · 1426 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 1157 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 1153 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6P5A · Drosophila P element transposase strand transfer complex · the same entry in another collection · chain K against K, 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 6P5A · PDBe 6P5A · UniProt Q7M3K2
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