MolNFT v1 · #161464 · protein + DNA
The complex structure of hsrosr-S4 (VNG0258/ROSR-S4)
6QFD · DNA-binding protein: “The complex structure of hsrosr-S4 (VNG0258/ROSR-S4)”. X-ray diffraction, 2 ligands (MN, SO4), 14 pockets (best druggability 0.84). MolNFT v1 #161464 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6QFD
- Type
- protein + DNA
- Length
- 570 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein; DNA (28-mer)
- UniProt
- Q9HSF4
- Ligands
- MN, SO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA-binding protein | protein | 115 | 67% helix, 10% strand | Q9HSF4 |
| B | DNA-binding protein | protein | 116 | 66% helix, 13% strand | Q9HSF4 |
| C | DNA-binding protein | protein | 112 | 68% helix, 11% strand | Q9HSF4 |
| E, G | DNA (28-mer) | dna | 28 | — | — |
| F, H | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, D, B, C, F
- SO4 · Sulfate ion · ion · 27 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.84 | 0.96 | 39 | empty |
| 2 | 91 | 0.76 | 0.97 | 32 | empty |
| 3 | 712 | 0.71 | 0.78 | 41 | empty |
| 4 | 685 | 0.68 | 0.77 | 41 | SO4 |
| 5 | 360 | 0.62 | 0.78 | 47 | MN |
Interfaces
17 interfaces between chains.
- A–B · 2116 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2050 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1291 Ų buried · 122 hydrogen bonds · nucleic-nucleic
- G–H · 1286 Ų buried · 134 hydrogen bonds · nucleic-nucleic
- A–F · 504 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6QFD · The complex structure of hsRosR-S4 (vng0258/RosR-S4) · 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 Q9HSF4
- Elsewhere: RCSB PDB 6QFD · PDBe 6QFD · UniProt Q9HSF4
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