Research workbench
Crystal structure of apo shwanavidin (P1 form)
Analyse Crystal structure of apo shwanavidin (P1 form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZH
- Type
- protein
- Length
- 697 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AVIDIN/STREPTAVIDIN
- UniProt
- Q12QS6
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AVIDIN/STREPTAVIDIN | protein | 115 | 3% helix, 60% strand | Q12QS6 |
| B | AVIDIN/STREPTAVIDIN | protein | 116 | 3% helix, 59% strand | Q12QS6 |
| C | AVIDIN/STREPTAVIDIN | protein | 117 | 3% helix, 62% strand | Q12QS6 |
| D | AVIDIN/STREPTAVIDIN | protein | 116 | 3% helix, 63% strand | Q12QS6 |
| E | AVIDIN/STREPTAVIDIN | protein | 116 | 3% helix, 63% strand | Q12QS6 |
| F | AVIDIN/STREPTAVIDIN | protein | 117 | 3% helix, 63% strand | Q12QS6 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.76 | 0.81 | 83 | empty |
| 2 | 346 | 0.65 | 0.80 | 40 | empty |
| 3 | 96 | 0.59 | 0.86 | 17 | empty |
| 4 | 97 | 0.57 | 0.85 | 19 | empty |
| 5 | 168 | 0.53 | 0.79 | 19 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1712 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1696 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1683 Ų buried · 24 hydrogen bonds · protein-protein
- C–F · 613 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 581 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3SZH · Crystal structure of apo shwanavidin (P1 form) · 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 Q12QS6
- Elsewhere: RCSB PDB 3SZH · PDBe 3SZH · UniProt Q12QS6
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