MolNFT v1 · #160656 · protein + DNA
Cryo-EM structure of HZTRANSIB/INTACT tir substrate DNA pre-reaction complex (prc)
6PQR · DNA-mediated transposase: “Cryo-EM structure of HZTRANSIB/INTACT tir substrate DNA pre-reaction complex (prc)”. Electron microscopy, 3 ligands (MG, ZN, K), 19 pockets (best druggability 0.86). MolNFT v1 #160656 on GenesisL1: 3D…
- PDB
- 6PQR
- Type
- protein + DNA
- Length
- 1,024 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-mediated transposase; DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*CP*GP*GP*TP*GP*GP*AP*T…
- UniProt
- B0F0C5
- Ligands
- MG, ZN, K
- Pockets
- 19 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA-mediated transposase | protein | 468 | 44% helix, 13% strand | B0F0C5 |
| B, E | DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP* AP*A)-3') | dna | 22 | — | — |
| C, F | DNA (5'- D(P*TP*TP*TP*TP*CP*GP*AP*TP*CP*CP*AP*CP*CP*GP*TP*GP*AP*GP*AP*TP*CP*TP *AP*G)-3') | dna | 22 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, D
- K · Potassium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.86 | 0.87 | 113 | K |
| 2 | 1181 | 0.77 | 0.79 | 82 | MG |
| 3 | 1169 | 0.76 | 0.78 | 81 | MG |
| 4 | 67 | 0.71 | 0.96 | 21 | empty |
| 5 | 79 | 0.69 | 0.94 | 21 | empty |
Interfaces
11 interfaces between chains.
- A–D · 999 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 943 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- E–F · 943 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- B–D · 531 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 531 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6PQR · Cryo-EM structure of HzTransib/intact 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 6PQR · PDBe 6PQR · UniProt B0F0C5
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