Research workbench
Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (imntail) at 1.2 a resolution
Analyse Crystal structure of the core streptavidin mutant V21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WZP
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- ZOF
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Streptavidin | protein | 123 | 9% helix, 55% strand | P22629 |
| B, D | Streptavidin | protein | 123 | 10% helix, 56% strand | P22629 |
Ligands and binding sites
- ZOF · 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid · ligand · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.65 | 0.88 | 23 | ZOF |
| 2 | 118 | 0.64 | 0.87 | 24 | ZOF |
| 3 | 149 | 0.61 | 0.84 | 26 | ZOF |
| 4 | 157 | 0.59 | 0.82 | 25 | ZOF |
| 5 | 202 | 0.56 | 0.80 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1651 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 531 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 212 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3WZP · Crystal structure of the core streptavidin mutant V21… · the same entry in another collection · 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 P22629
- Elsewhere: RCSB PDB 3WZP · PDBe 3WZP · UniProt P22629
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