Research workbench
Avidin-norbioitn complex
Analyse Avidin-norbioitn complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LDO
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin
- UniProt
- P02701
- Ligands
- SNR, NAG
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Avidin | protein | 121 | 7% helix, 50% strand | P02701 |
Ligands and binding sites
- SNR · Norbiotin · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.58 | 0.82 | 20 | SNR |
| 2 | 216 | 0.57 | 0.79 | 32 | SNR |
| 3 | 50 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 145 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P02701
- Elsewhere: RCSB PDB 1LDO · PDBe 1LDO · UniProt P02701
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