MolNFT v1 · #1232 · protein
Three-dimensional structure of the tetragonal crystal form of egg- white avidin in its functional complex with biotin at 2.7 ångströms resolution
1AVD: “Three-dimensional structure of the tetragonal crystal form of egg- white avidin in its functional complex…”. X-ray diffraction, 2 ligands (BTN, NAG), 4 pockets (best druggability 0.58). MolNFT v1 #1232 on GenesisL1: 3D structure…
- PDB
- 1AVD
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin
- UniProt
- P02701
- Ligands
- BTN, NAG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Avidin | protein | 123 | 2% helix, 48% strand | P02701 |
| B | Avidin | protein | 124 | 5% helix, 48% strand | P02701 |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.58 | 0.84 | 20 | BTN |
| 2 | 134 | 0.57 | 0.83 | 24 | BTN |
| 3 | 69 | 0.27 | 0.71 | 14 | empty |
| 4 | 56 | 0.25 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 148 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1AVD · Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its… · the same entry in another collection · chain A against A, TM-score 1.00
- P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 1AVD · PDBe 1AVD · UniProt P02701
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