Research workbench
Structure of the C. crescentus drid C-domain bound to ssdna
Analyse Structure of the C. crescentus drid C-domain bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U02
- Type
- protein + DNA
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wyl domain-containing protein; DNA (5'-D(P*AP*CP*G)-3')
- UniProt
- Q9A999
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Wyl domain-containing protein | protein | 193 | 27% helix, 25% strand | Q9A999 |
| H | DNA (5'-D(P*AP*CP*G)-3') | dna | 3 | — | — |
| M | Wyl domain-containing protein | protein | 192 | 29% helix, 34% strand | Q9A999 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, M
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 | 1137 | 0.84 | 0.85 | 92 | SO4 |
| 2 | 108 | 0.37 | 0.74 | 21 | SO4 |
Interfaces
2 interfaces between chains.
- B–M · 2573 Ų buried · 18 hydrogen bonds · protein-protein
- H–M · 661 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7U02 · Structure of the C. crescentus DriD C-domain bound to ssDNA · the same entry in another collection · chain B against B, 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 Q9A999
- Elsewhere: RCSB PDB 7U02 · PDBe 7U02 · UniProt Q9A999
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