MolNFT v1 · #109164 · protein + DNA
Crystal structure of E. faecalis DNA binding domain liar wild type complexed with 22BP DNA
4WUH · Response regulator receiver domain protein: “Crystal structure of E. faecalis DNA binding domain liar wild type complexed with 22BP DNA”. X-ray diffraction, 2 pockets (best druggability 0.63). MolNFT v1 #109164 on GenesisL1: 3D…
- 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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