Research workbench
Crystal structure of E. faecalis DNA binding domain liar wild type complexed with 22BP DNA
Analyse Crystal structure of E. faecalis DNA binding domain liar wild type complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WUH
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator receiver domain protein; DNA (5'…
- UniProt
- D4EMQ0
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Response regulator receiver domain protein | protein | 68 | 66% helix, 0% strand | D4EMQ0 |
| G | DNA (5'- D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3') | dna | 17 | — | — |
| H | DNA (5'-D(P*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, G, H
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 | 364 | 0.63 | 0.79 | 35 | GOL |
| 2 | 139 | 0.41 | 0.75 | 21 | empty |
Interfaces
9 interfaces between chains.
- G–H · 478 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–B · 467 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–G · 349 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–H · 335 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4WUH · Crystal structure of E. faecalis DNA binding domain LiaR wild type complexed with 22bp 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 D4EMQ0
- Elsewhere: RCSB PDB 4WUH · PDBe 4WUH · UniProt D4EMQ0
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