MolNFT v1 · #146919 · protein + DNA
Hermes transposase deletion dimer complex with (C/G) DNA and CA2+
6DWY: “Hermes transposase deletion dimer complex with (C/G) DNA and CA2+”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.65). MolNFT v1 #146919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DWY
- Type
- protein + DNA
- Length
- 531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hermes transposase; DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)- 3'); DNA…
- UniProt
- Q25438
- Ligands
- CA
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hermes transposase | protein | 483 | 58% helix, 8% strand | Q25438 |
| B | DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)- 3') | dna | 16 | — | — |
| C | DNA (26-mer) | dna | 25 | — | — |
| D | DNA (5'-D(*C*GP*CP*GP*TP*GP*AP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.65 | 0.78 | 36 | empty |
| 2 | 204 | 0.62 | 0.82 | 28 | empty |
| 3 | 256 | 0.60 | 0.80 | 26 | empty |
| 4 | 121 | 0.54 | 0.83 | 22 | empty |
| 5 | 266 | 0.48 | 0.73 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1076 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 704 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–B · 528 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 352 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- A–D · 220 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6DWY · Hermes transposase deletion dimer complex with (C/G) DNA and Ca2+ · 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 6DWY · PDBe 6DWY · UniProt Q25438
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