Research workbench
Designed armadillo repeat protein internal LOCK1 fused to target peptide krkrklkfkr
Analyse Designed armadillo repeat protein internal LOCK1 fused to target peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9O
- Type
- protein
- Length
- 2,034 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr
- Ligands
- CA
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr | protein | 340 | 70% helix, 0% strand | — |
| B, E | Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr | protein | 341 | 70% helix, 0% strand | — |
| C | Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr | protein | 335 | 72% helix, 0% strand | — |
| D | Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr | protein | 334 | 72% helix, 0% strand | — |
| F | Designed armadillo repeat protein with internal LOCK1 fused to target peptide krkrklkfkr | protein | 343 | 71% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.84 | 0.85 | 124 | CA |
| 2 | 578 | 0.79 | 0.85 | 78 | EDO |
| 3 | 542 | 0.78 | 0.85 | 51 | empty |
| 4 | 458 | 0.76 | 0.85 | 46 | empty |
| 5 | 420 | 0.75 | 0.86 | 72 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1655 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1464 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 742 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 663 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 265 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6S9O · Designed Armadillo Repeat protein internal Lock1 fused to target peptide KRKRKLKFKR · 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
- Elsewhere: RCSB PDB 6S9O · PDBe 6S9O
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