MolNFT v1 · #105070 · protein + DNA
Computational design of co-assembling protein-DNA nanowires
4QTR · Dualenh: “Computational design of co-assembling protein-DNA nanowires”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #105070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QTR
- Type
- protein + DNA
- Length
- 284 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dualenh; DNA (5'- D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3'); DNA (5'…
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dualenh | protein | 55 | 69% helix, 0% strand | — |
| B | Dualenh | protein | 54 | 76% helix, 0% strand | — |
| C | Dualenh | protein | 57 | 68% helix, 0% strand | — |
| E | DNA (5'- D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3') | dna | 15 | — | — |
| F, H | DNA (5'- D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3') | dna | 16 | — | — |
| G | DNA (5'- D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3') | dna | 16 | — | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.78 | 0.81 | 93 | empty |
| 2 | 931 | 0.76 | 0.79 | 88 | empty |
| 3 | 159 | 0.56 | 0.81 | 22 | empty |
| 4 | 113 | 0.42 | 0.77 | 15 | empty |
| 5 | 66 | 0.26 | 0.72 | 12 | empty |
Interfaces
12 interfaces between chains.
- G–H · 639 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- E–F · 618 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- B–C · 444 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 279 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–G · 273 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4QTR · Computational design of co-assembling protein-DNA nanowires · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 4QTR · PDBe 4QTR
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