MolNFT v1 · #143944 · protein + DNA
Structure of sihf bound to an 8BP palindromic DNA
6BEK · SCO1480: “Structure of sihf bound to an 8BP palindromic DNA”. X-ray diffraction, 1 ligand (K), 2 pockets (best druggability 0.53). MolNFT v1 #143944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BEK
- Type
- protein + DNA
- Length
- 213 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCO1480; DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
- UniProt
- Q9KXR9
- Ligands
- K
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SCO1480 | protein | 92 | 66% helix, 2% strand | Q9KXR9 |
| B, C, E, F | DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3') | dna | 8 | — | — |
| D | SCO1480 | protein | 89 | 65% helix, 2% strand | Q9KXR9 |
Ligands and binding sites
- 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.53 | 0.77 | 22 | empty |
| 2 | 56 | 0.29 | 0.76 | 14 | empty |
Interfaces
7 interfaces between chains.
- E–F · 385 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- B–C · 380 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–C · 276 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–F · 273 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 163 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6BEK · Structure of sIHF bound to an 8bp palindromic DNA · 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 Q9KXR9
- Elsewhere: RCSB PDB 6BEK · PDBe 6BEK · UniProt Q9KXR9
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