Research workbench
The X-ray structure of the DNase I-D(GGTATACC)2 complex at 2.3 ångströms resolution
Analyse The X-ray structure of the DNase I-D(GGTATACC)2 complex at 2.3 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DNK
- Type
- protein + DNA
- Length
- 265 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3'); DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'); Protein…
- UniProt
- P00639
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3') | dna | 7 | — | — |
| C | DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3') | dna | 8 | — | — |
| A | Protein (deoxyribonuclease I (DNase I) (E.C.3.1.21.1)) | protein | 250 | 30% helix, 30% strand | P00639 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
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 | 174 | 0.51 | 0.78 | 24 | empty |
| 2 | 57 | 0.40 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 522 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 339 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- B–A · 253 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1DNK · The X-ray structure of the DNase I-D(GGTATACC)2 complex at 2.3 ångströms resolution · the same entry in another collection · chain B against B, TM-score 1.00
- P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · 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 P00639
- Elsewhere: RCSB PDB 1DNK · PDBe 1DNK · UniProt P00639
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