Research workbench
Crystallographic structure of duck ovotransferrin at 2.3 ångströms resolution
Analyse Crystallographic structure of duck ovotransferrin at 2.3 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DOT
- Type
- protein
- Length
- 686 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Duck ovotransferrin
- UniProt
- P56410
- Ligands
- NAG, FUC, FE, CO3
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Duck ovotransferrin | protein | 686 | 30% helix, 17% strand | P56410 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- FE · Fe (III) ion · metal · 2 copies · chains A
- CO3 · Carbonate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.80 | 0.94 | 34 | empty |
| 2 | 248 | 0.71 | 0.86 | 38 | empty |
| 3 | 450 | 0.65 | 0.78 | 60 | empty |
| 4 | 214 | 0.59 | 0.80 | 31 | empty |
| 5 | 141 | 0.50 | 0.79 | 31 | empty |
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 1DOT · Crystallographic structure of duck ovotransferrin at 2.3 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P56410 · AlphaFold monomer V2.0 prediction for ovotransferrin (P56410) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P56410
- Elsewhere: RCSB PDB 1DOT · PDBe 1DOT · UniProt P56410
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