MolNFT v1 · #12577 · protein
An engineered streptavidin with improved affinity for the strep-tag II peptide : SAM2-strepii
1KL5: “An engineered streptavidin with improved affinity for the strep-tag II peptide : SAM2-strepii”. X-ray diffraction, 6 pockets (best druggability 0.61). MolNFT v1 #12577 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KL5
- Type
- protein
- Length
- 502 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin; Strep-tag II
- UniProt
- P22629
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 121 | 7% helix, 56% strand | P22629 |
| B, C | Streptavidin | protein | 120 | 8% helix, 56% strand | P22629 |
| D | Streptavidin | protein | 119 | 8% helix, 57% strand | P22629 |
| E | Strep-tag II | protein | 5 | 0% helix, 0% strand | — |
| F | Strep-tag II | protein | 5 | 60% helix, 0% strand | — |
| G, H | Strep-tag II | 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 | 281 | 0.61 | 0.80 | 32 | empty |
| 2 | 239 | 0.59 | 0.80 | 31 | empty |
| 3 | 223 | 0.57 | 0.79 | 37 | empty |
| 4 | 155 | 0.51 | 0.79 | 35 | empty |
| 5 | 101 | 0.33 | 0.72 | 22 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1603 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1586 Ų buried · 20 hydrogen bonds · protein-protein
- C–G · 453 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 442 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 430 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1KL5 · an engineered streptavidin with improved affinity for the strep-tag II peptide… · 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 1KL5 · PDBe 1KL5 · UniProt P22629
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