MolNFT v1 · #115447 · protein
Signal recognition particle receptor srb-GTP/SRX complex from chaetomium thermophilum
5CK3 · Srx domain: “Signal recognition particle receptor srb-GTP/SRX complex from chaetomium thermophilum”. X-ray diffraction, 3 ligands (GTP, MG, SO4), 20 pockets (best druggability 0.76). MolNFT v1 #115447 on GenesisL1: 3D structure…
- PDB
- 5CK3
- Type
- protein
- Length
- 991 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Srx domain; Putative signal recognition particle protein
- UniProt
- G0S1R8, G0S401
- Ligands
- GTP, MG, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Srx domain | protein | 135 | 36% helix, 19% strand | G0S1R8 |
| B | Putative signal recognition particle protein | protein | 270 | 29% helix, 16% strand | G0S401 |
| C | Srx domain | protein | 105 | 42% helix, 21% strand | G0S1R8 |
| D | Putative signal recognition particle protein | protein | 230 | 31% helix, 17% strand | G0S401 |
| E | Srx domain | protein | 104 | 41% helix, 19% strand | G0S1R8 |
| F | Putative signal recognition particle protein | protein | 147 | 42% helix, 6% strand | G0S401 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains B, D, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, D, F
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.76 | 0.80 | 85 | empty |
| 2 | 73 | 0.68 | 0.94 | 17 | empty |
| 3 | 328 | 0.61 | 0.78 | 35 | empty |
| 4 | 277 | 0.58 | 0.78 | 41 | MG, GTP |
| 5 | 248 | 0.57 | 0.78 | 44 | MG, GTP |
Interfaces
5 interfaces between chains.
- A–B · 1367 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1090 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 943 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 539 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 346 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5CK3 · Signal recognition particle receptor SRb-GTP/SRX complex from Chaetomium thermophilum · 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 G0S1R8
- Every structure of UniProt G0S401
- Elsewhere: RCSB PDB 5CK3 · PDBe 5CK3 · UniProt G0S1R8 · UniProt G0S401
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