MolNFT v1 · #160659 · protein + DNA
Cryo-EM structure of HZTRANSIB/NICKED tir substrate DNA pre-reaction complex (prc)
6PQU · DNA-mediated transposase: “Cryo-EM structure of HZTRANSIB/NICKED tir substrate DNA pre-reaction complex (prc)”. Electron microscopy, 3 ligands (MG, ZN, K), 15 pockets (best druggability 0.80). MolNFT v1 #160659 on GenesisL1: 3D…
- PDB
- 6PQU
- Type
- protein + DNA
- Length
- 1,060 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-mediated transposase; DNA (5'-D(P*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*T)- 3')…
- UniProt
- B0F0C5
- Ligands
- MG, ZN, K
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA-mediated transposase | protein | 468 | 45% helix, 12% strand | B0F0C5 |
| B, F | DNA (5'-D(P*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*T)- 3') | dna | 15 | — | — |
| 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 | 31 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E
- ZN · Zinc ion · metal · 2 copies · chains A, E
- K · Potassium ion · metal · 2 copies · chains A, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.80 | 0.87 | 67 | empty |
| 2 | 885 | 0.80 | 0.83 | 68 | MG, K |
| 3 | 434 | 0.79 | 0.88 | 53 | empty |
| 4 | 1198 | 0.78 | 0.80 | 80 | MG, K |
| 5 | 237 | 0.62 | 0.81 | 41 | empty |
Interfaces
17 interfaces between chains.
- A–E · 987 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- F–H · 716 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- G–H · 702 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- C–D · 699 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PQU · Cryo-EM structure of HzTransib/nicked TIR substrate DNA pre-reaction complex (PRC) · 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 6PQU · PDBe 6PQU · UniProt B0F0C5
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