Research workbench
Streptavidin mutant Y43A with iminobiotin at 1.8A resolution
Analyse Streptavidin mutant Y43A with iminobiotin at 1.8A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NC9
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- IMI
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 5% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 114 | 8% helix, 57% strand | P22629 |
| C, D | Streptavidin | protein | 111 | 5% helix, 59% strand | P22629 |
Ligands and binding sites
- IMI · 2-iminobiotin · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.69 | 0.83 | 48 | IMI |
| 2 | 366 | 0.63 | 0.78 | 42 | empty |
| 3 | 312 | 0.61 | 0.79 | 39 | empty |
| 4 | 305 | 0.60 | 0.78 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1659 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1607 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 463 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1NC9 · Streptavidin mutant Y43A with iminobiotin at 1.8A resolution · 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 1NC9 · PDBe 1NC9 · UniProt P22629
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