Research workbench
Crystal structure of E. faecalis DNA binding domain LIARD191N complexed with 22BP DNA
Analyse Crystal structure of E. faecalis DNA binding domain LIARD191N complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WU4
- Type
- protein + DNA
- Length
- 170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator receiver domain protein; DNA (5'…
- UniProt
- R3G073
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 3 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 | R3G073 |
| 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*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3') | dna | 17 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 304 | 0.61 | 0.80 | 32 | GOL |
| 2 | 144 | 0.41 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- G–H · 748 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–B · 459 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 428 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–G · 345 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–H · 338 Ų buried · 7 hydrogen bonds · protein-nucleic
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 R3G073
- Elsewhere: RCSB PDB 4WU4 · PDBe 4WU4 · UniProt R3G073
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