MolNFT v1 · #160670 · protein + DNA
Cryo-EM structure of hztransib strand transfer complex (stc)
6PR5 · DNA-mediated transposase: “Cryo-EM structure of hztransib strand transfer complex (stc)”. Electron microscopy, 2 ligands (MG, ZN), 13 pockets (best druggability 0.88). MolNFT v1 #160670 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PR5
- Type
- protein + DNA
- Length
- 1,084 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-mediated transposase; DNA (5'- D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*TP*CP*A…
- UniProt
- B0F0C5
- Ligands
- MG, ZN
- Pockets
- 13 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA-mediated transposase | protein | 480 | 45% helix, 13% strand | B0F0C5 |
| B | DNA (5'- D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*AP*GP*AP*TP*CP*TP*CP*A)-3') | dna | 16 | — | — |
| 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 | DNA (30-mer) | dna | 30 | — | — |
| F | DNA (5'-D(P*TP*TP*TP*TP*CP*GP*AP*TP*C)-3') | dna | 9 | — | — |
| H | DNA (39-mer) | dna | 37 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E, F, H
- ZN · Zinc ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.88 | 0.90 | 107 | empty |
| 2 | 954 | 0.76 | 0.79 | 76 | empty |
| 3 | 748 | 0.74 | 0.79 | 67 | empty |
| 4 | 321 | 0.73 | 0.86 | 37 | empty |
| 5 | 386 | 0.71 | 0.83 | 35 | empty |
Interfaces
18 interfaces between chains.
- A–E · 1883 Ų buried · 13 hydrogen bonds · protein-protein
- E–D · 1372 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–H · 1339 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 908 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–H · 888 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 6PR5 · Cryo-EM structure of HzTransib strand transfer complex (STC) · 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 6PR5 · PDBe 6PR5 · UniProt B0F0C5
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