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Structure based engineering of streptavidin monomer with a reduced biotin dissociation rate
Analyse Structure based engineering of streptavidin monomer with a reduced biotin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNJ
- Type
- protein
- Length
- 453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- STREPTAVIDIN/RHIZAVIDIN hybrid
- Ligands
- BTN, ZN
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | STREPTAVIDIN/RHIZAVIDIN hybrid | protein | 115 | 3% helix, 62% strand | — |
| B | STREPTAVIDIN/RHIZAVIDIN hybrid | protein | 114 | 4% helix, 63% strand | — |
| C | STREPTAVIDIN/RHIZAVIDIN hybrid | protein | 111 | 0% helix, 66% strand | — |
| D | STREPTAVIDIN/RHIZAVIDIN hybrid | protein | 113 | 0% helix, 62% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 9 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.73 | 0.98 | 18 | empty |
| 2 | 59 | 0.71 | 0.98 | 20 | empty |
| 3 | 865 | 0.71 | 0.77 | 78 | empty |
| 4 | 101 | 0.52 | 0.82 | 18 | BTN |
| 5 | 100 | 0.51 | 0.82 | 18 | BTN, ZN |
Interfaces
5 interfaces between chains.
- A–C · 567 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 87 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4JNJ · Structure based engineering of streptavidin monomer with a reduced biotin dissociation… · 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
- Elsewhere: RCSB PDB 4JNJ · PDBe 4JNJ
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