Research workbench
Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S
Analyse Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y53
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin-related protein 4/5
- UniProt
- P56734
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | Avidin-related protein 4/5 | protein | 120 | 8% helix, 50% strand | P56734 |
Ligands and binding sites
- FMT · Formic acid · additive · 6 copies · chains X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.55 | 0.83 | 20 | FMT |
| 2 | 128 | 0.54 | 0.82 | 22 | FMT |
Interfaces
1 interface between chains.
- X–Y · 1691 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1Y53 · Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S · the same entry in another collection · chain X against X, TM-score 1.00
- P56734 · AlphaFold monomer V2.0 prediction for avidin-related protein 4/5 (P56734) · a predicted model of the same protein · chain X against A, TM-score 0.99
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 P56734
- Elsewhere: RCSB PDB 1Y53 · PDBe 1Y53 · UniProt P56734
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