MolNFT v1 · #12575 · protein
An engineered streptavidin with improved affinity for the strep-tag II peptide : SAM1-strepii
1KL3: “An engineered streptavidin with improved affinity for the strep-tag II peptide : SAM1-strepii”. X-ray diffraction, 6 pockets (best druggability 0.62). MolNFT v1 #12575 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KL3
- Type
- protein
- Length
- 504 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Strep-tag II peptide
- UniProt
- P22629
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 7% helix, 55% strand | P22629 |
| B, C | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| D | Streptavidin | protein | 119 | 8% helix, 56% strand | P22629 |
| E | Strep-tag II peptide | protein | 6 | 50% helix, 0% strand | — |
| F, G, H | Strep-tag II peptide | protein | 6 | 50% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.62 | 0.80 | 34 | empty |
| 2 | 270 | 0.60 | 0.79 | 38 | empty |
| 3 | 176 | 0.58 | 0.82 | 27 | empty |
| 4 | 240 | 0.58 | 0.79 | 34 | empty |
| 5 | 89 | 0.32 | 0.72 | 18 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1614 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1600 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 441 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 432 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 421 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1KL3 · an engineered streptavidin with improved affinity for the strep-tag II peptide… · the same entry in another collection · chain B against B, 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 1KL3 · PDBe 1KL3 · UniProt P22629
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