MolNFT v1 · #160662 · protein + DNA
Cryo-EM structure of HZTRANSIB/NICKED tir substrate DNA hairpin forming complex (hfc)
6PQX · DNA-mediated transposase: “Cryo-EM structure of HZTRANSIB/NICKED tir substrate DNA hairpin forming complex (hfc)”. Electron microscopy, 1 ligand (CA), 17 pockets (best druggability 0.86). MolNFT v1 #160662 on GenesisL1: 3D…
- PDB
- 6PQX
- Type
- protein + DNA
- Length
- 1,080 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-mediated transposase; DNA (5'-D(P*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*T)-3'); DNA…
- UniProt
- B0F0C5
- Ligands
- CA
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA-mediated transposase | protein | 480 | 48% helix, 12% strand | B0F0C5 |
| B, F | DNA (5'-D(P*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*T)-3') | dna | 14 | — | — |
| C, G | DNA (5'- D(P*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*AP*A)-3') | dna | 16 | — | — |
| D, H | Tir substrate DNA transferred strand | dna | 30 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, B, E, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.86 | 0.91 | 73 | empty |
| 2 | 303 | 0.79 | 0.90 | 45 | CA |
| 3 | 980 | 0.78 | 0.80 | 94 | empty |
| 4 | 880 | 0.76 | 0.80 | 79 | empty |
| 5 | 207 | 0.72 | 0.89 | 27 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1759 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1244 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–H · 1201 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 815 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–G · 768 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6PQX · Cryo-EM structure of HzTransib/nicked TIR substrate DNA hairpin forming complex (HFC) · 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 B0F0C5
- Elsewhere: RCSB PDB 6PQX · PDBe 6PQX · UniProt B0F0C5
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