MolNFT v1 · #146917 · protein + DNA
Hermes transposase deletion dimer complex with (A/T) DNA and MN2+
6DWW: “Hermes transposase deletion dimer complex with (A/T) DNA and MN2+”. X-ray diffraction, 1 ligand (MN), 8 pockets (best druggability 0.65). MolNFT v1 #146917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DWW
- 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
- MN
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hermes transposase | protein | 483 | 61% 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 (25-mer) | dna | 25 | — | — |
| D | DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3') | dna | 7 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.65 | 0.78 | 31 | empty |
| 2 | 298 | 0.64 | 0.80 | 33 | empty |
| 3 | 101 | 0.56 | 0.86 | 23 | empty |
| 4 | 103 | 0.56 | 0.85 | 21 | empty |
| 5 | 202 | 0.51 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–C · 968 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 716 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- A–B · 528 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 381 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–D · 229 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6DWW · Hermes transposase deletion dimer complex with (A/T) DNA and Mn2+ · 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 6DWW · PDBe 6DWW · UniProt Q25438
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