MolNFT v1 · #12391 · protein
An engineered streptavidin with improved affinity for the strep-tag II peptide: apo-SAM1
1KFF: “An engineered streptavidin with improved affinity for the strep-tag II peptide: apo-SAM1”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #12391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KFF
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 8% helix, 57% strand | P22629 |
| B | Streptavidin | protein | 120 | 8% helix, 56% strand | P22629 |
| C, D | Streptavidin | protein | 119 | 8% helix, 57% strand | P22629 |
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 | 406 | 0.63 | 0.78 | 45 | empty |
| 2 | 390 | 0.63 | 0.78 | 47 | empty |
| 3 | 328 | 0.63 | 0.79 | 43 | empty |
| 4 | 347 | 0.62 | 0.79 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1589 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1585 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1KFF · An engineered streptavidin with improved affinity for the strep-tag II peptide: apo-SAM1 · the same entry in another collection · chain D against D, 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 1KFF · PDBe 1KFF · UniProt P22629
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