MolNFT v1 · #146920 · protein + DNA
Hermes transposase deletion dimer complex with (C/G) DNA
6DWZ: “Hermes transposase deletion dimer complex with (C/G) DNA”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #146920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DWZ
- Type
- protein + DNA
- Length
- 1,046 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hermes transposase; DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)- 3'); DNA…
- UniProt
- Q25438
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hermes transposase | protein | 476 | 57% helix, 8% strand | Q25438 |
| B, F | DNA (5'-D(*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)- 3') | dna | 15 | — | — |
| C, G | DNA (26-mer) | dna | 25 | — | — |
| D, H | DNA (5'-D(*GP*CP*GP*TP*GP*AP*C)-3') | dna | 7 | — | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.79 | 0.89 | 45 | empty |
| 2 | 610 | 0.79 | 0.85 | 56 | empty |
| 3 | 423 | 0.77 | 0.87 | 49 | empty |
| 4 | 184 | 0.71 | 0.90 | 29 | empty |
| 5 | 224 | 0.70 | 0.87 | 30 | empty |
Interfaces
15 interfaces between chains.
- A–E · 4274 Ų buried · 29 hydrogen bonds · protein-protein
- E–G · 777 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 754 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–G · 681 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- B–C · 672 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DWZ · Hermes transposase deletion dimer complex with (C/G) DNA · 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 Q25438
- Elsewhere: RCSB PDB 6DWZ · PDBe 6DWZ · UniProt Q25438
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