MolNFT v1 · #149921 · protein + DNA
Adhesin domain of prgb from enterococcus faecalis bound to DNA
6GED: “Adhesin domain of prgb from enterococcus faecalis bound to DNA”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.58). MolNFT v1 #149921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GED
- Type
- protein + DNA
- Length
- 315 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prgb; DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3'); DNA…
- UniProt
- Q04112
- Ligands
- NA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prgb | protein | 295 | 8% helix, 40% strand | Q04112 |
| C | DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.58 | 0.82 | 24 | empty |
| 2 | 135 | 0.51 | 0.81 | 16 | empty |
| 3 | 249 | 0.51 | 0.76 | 26 | empty |
| 4 | 113 | 0.38 | 0.75 | 16 | EDO |
Interfaces
3 interfaces between chains.
- C–D · 438 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–C · 260 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 178 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6GED · Adhesin domain of PrgB from Enterococcus faecalis bound to 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 Q04112
- Elsewhere: RCSB PDB 6GED · PDBe 6GED · UniProt Q04112
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