MolNFT v1 · #115449 · protein
Signal recognition particle receptor srb-GDP-mg from chaetomium thermophilum
5CK5 · Putative signal recognition particle protein: “Signal recognition particle receptor srb-GDP-mg from chaetomium thermophilum”. X-ray diffraction, 2 ligands (GDP, MG), 4 pockets (best druggability 0.57). MolNFT v1 #115449 on…
- PDB
- 5CK5
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative signal recognition particle protein
- UniProt
- G0S401
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative signal recognition particle protein | protein | 221 | 40% helix, 17% strand | G0S401 |
| B | Putative signal recognition particle protein | protein | 221 | 38% helix, 18% strand | G0S401 |
| C | Putative signal recognition particle protein | protein | 215 | 39% helix, 16% strand | G0S401 |
| D | Putative signal recognition particle protein | protein | 206 | 42% helix, 17% strand | G0S401 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.57 | 0.76 | 33 | empty |
| 2 | 381 | 0.54 | 0.73 | 44 | GDP, MG |
| 3 | 84 | 0.31 | 0.73 | 16 | empty |
| 4 | 50 | 0.30 | 0.76 | 10 | empty |
Interfaces
4 interfaces between chains.
- A–B · 460 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 119 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
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 G0S401
- Elsewhere: RCSB PDB 5CK5 · PDBe 5CK5 · UniProt G0S401
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