MolNFT v1 · #168421 · protein + DNA
Coordinates of nanr dimer fitted in hexameric nanr-DNA hetero-complex cryo-EM MAP
6WG7 · DNA (35-mer): “Coordinates of nanr dimer fitted in hexameric nanr-DNA hetero-complex cryo-EM MAP”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #168421 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WG7
- Type
- protein + DNA
- Length
- 1,411 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (35-mer); Hth-type transcriptional repressor nanr
- UniProt
- J7QHT8
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (35-mer) | dna | 35 | — | — |
| B | DNA (35-mer) | dna | 35 | — | — |
| C, E, F | Hth-type transcriptional repressor nanr | protein | 228 | 64% helix, 0% strand | J7QHT8 |
| D, G, H | Hth-type transcriptional repressor nanr | protein | 219 | 67% helix, 0% strand | J7QHT8 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.84 | 0.87 | 92 | empty |
| 2 | 857 | 0.83 | 0.85 | 90 | empty |
| 3 | 1057 | 0.83 | 0.84 | 100 | empty |
| 4 | 567 | 0.82 | 0.87 | 59 | empty |
| 5 | 366 | 0.82 | 0.91 | 38 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1594 Ų buried · 161 hydrogen bonds · nucleic-nucleic
- F–H · 1581 Ų buried · 10 hydrogen bonds · protein-protein
- E–G · 1577 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1574 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 6WG7 · Coordinates of NanR dimer fitted in Hexameric NanR-DNA hetero-complex cryo-EM map · the same entry in another collection · chain E against E, 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 J7QHT8
- Elsewhere: RCSB PDB 6WG7 · PDBe 6WG7 · UniProt J7QHT8
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