MolNFT v1 · #137956 · protein
C. japonica N-domain, selenomethionine mutant
5W4D · P-granule scaffold protein: “C. japonica N-domain, selenomethionine mutant”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.73). MolNFT v1 #137956 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W4D
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-granule scaffold protein
- UniProt
- H2W791
- Ligands
- CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-granule scaffold protein | protein | 211 | 69% helix, 3% strand | H2W791 |
| B | P-granule scaffold protein | protein | 215 | 66% helix, 3% strand | H2W791 |
| C | P-granule scaffold protein | protein | 208 | 66% helix, 3% strand | H2W791 |
| D | P-granule scaffold protein | protein | 212 | 69% helix, 3% strand | H2W791 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
- IMD · Imidazole · additive · 5 copies · chains B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.73 | 0.83 | 48 | empty |
| 2 | 510 | 0.72 | 0.81 | 57 | PEG, CL |
| 3 | 298 | 0.63 | 0.80 | 36 | PEG |
| 4 | 314 | 0.61 | 0.79 | 43 | empty |
| 5 | 236 | 0.60 | 0.80 | 35 | empty |
Interfaces
4 interfaces between chains.
- B–D · 931 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 928 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 666 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 579 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5W4D · C. japonica N-domain, Selenomethionine mutant · 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 5W4D · PDBe 5W4D · UniProt H2W791
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