MolNFT v1 · #51805 · protein + DNA
Crystal structure of the ISHP608 transposase in complex with left end 26-mer DNA and manganese
2VIC · Transposase orfa: “Crystal structure of the ISHP608 transposase in complex with left end 26-mer DNA and manganese”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.60). MolNFT v1 #51805 on GenesisL1: 3D structure…
- PDB
- 2VIC
- Type
- protein + DNA
- Length
- 330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase orfa; 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP…
- UniProt
- Q933Z0
- Ligands
- MN
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposase orfa | protein | 151 | 43% helix, 23% strand | Q933Z0 |
| B | Transposase orfa | protein | 128 | 41% helix, 27% strand | Q933Z0 |
| C | 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' | dna | 25 | — | — |
| D | 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' | dna | 26 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.60 | 0.80 | 27 | empty |
| 2 | 297 | 0.55 | 0.76 | 36 | empty |
| 3 | 229 | 0.55 | 0.78 | 21 | empty |
| 4 | 79 | 0.34 | 0.76 | 21 | empty |
| 5 | 70 | 0.32 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2117 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 951 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 924 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 643 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 613 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2VIC · CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and… · 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 Q933Z0
- Elsewhere: RCSB PDB 2VIC · PDBe 2VIC · UniProt Q933Z0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.