MolNFT v1 · #163660 · protein
Designed armadillo repeat protein LOCK2 fused to target peptide krkrkakitw
6S9M · LOCK2_KRKRKAKITW: “Designed armadillo repeat protein LOCK2 fused to target peptide krkrkakitw”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.79). MolNFT v1 #163660 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6S9M
- Type
- protein
- Length
- 1,796 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LOCK2_KRKRKAKITW
- Ligands
- CA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | LOCK2_KRKRKAKITW | protein | 300 | 69% helix, 0% strand | — |
| B | LOCK2_KRKRKAKITW | protein | 299 | 69% helix, 1% strand | — |
| D, F | LOCK2_KRKRKAKITW | protein | 298 | 69% helix, 1% strand | — |
| E | LOCK2_KRKRKAKITW | protein | 301 | 69% helix, 1% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, E, B, C, D, F
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, E, B, D, F
- PGE · Triethylene glycol · additive · 3 copies · chains C, D, A, E
- PG4 · Tetraethylene glycol · additive · 3 copies · chains B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.79 | 0.85 | 50 | EDO, PGE |
| 2 | 736 | 0.77 | 0.81 | 74 | empty |
| 3 | 465 | 0.77 | 0.85 | 51 | empty |
| 4 | 391 | 0.76 | 0.87 | 65 | PG4 |
| 5 | 337 | 0.69 | 0.83 | 57 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1498 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 1393 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 927 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S9M · Designed Armadillo Repeat protein Lock2 fused to target peptide KRKRKAKITW · the same entry in another collection · chain C against C, 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 6S9M · PDBe 6S9M
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