Research workbench
C. japonica N-domain
Analyse C. japonica N-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W4A
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-granule scaffold
- UniProt
- H2W791
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | P-granule scaffold | protein | 212 | 67% helix, 3% strand | H2W791 |
| B | P-granule scaffold | protein | 215 | 66% helix, 3% strand | H2W791 |
| C | P-granule scaffold | protein | 214 | 64% helix, 3% strand | H2W791 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- IMD · Imidazole · additive · 5 copies · chains B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.72 | 0.83 | 44 | empty |
| 2 | 465 | 0.71 | 0.81 | 56 | EDO, PGE |
| 3 | 327 | 0.66 | 0.81 | 47 | EDO |
| 4 | 258 | 0.61 | 0.80 | 35 | PEG |
| 5 | 241 | 0.61 | 0.80 | 36 | PG4 |
Interfaces
4 interfaces between chains.
- A–C · 925 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 922 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 651 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 600 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5W4A · C. japonica N-domain · 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 H2W791
- Elsewhere: RCSB PDB 5W4A · PDBe 5W4A · UniProt H2W791
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