Research workbench
Crystallographic refinement and structure of DNase I at 2 ångströms resolution
Analyse Crystallographic refinement and structure of DNase I at 2 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNI
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribonuclease I
- EC
- 3.1.21.1
- UniProt
- P00639
- Ligands
- BMA, NAG, GLA, MAN, CA
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribonuclease I (EC 3.1.21.1) | protein | 258 | 29% helix, 29% strand | P00639 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 3 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- GLA · alpha-D-galactopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.28 | 0.72 | 24 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3DNI · Crystallographic refinement and structure of DNase I at 2 ångströms resolution · the same entry in another collection · chain A against A, 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 3DNI · PDBe 3DNI · UniProt P00639
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