MolNFT v1 · #32765 · protein
Gmppcp complex of srp GTPase ffh ng domain at ultra-high resolution
2C04 · Signal recognition particle protein: “Gmppcp complex of srp GTPase ffh ng domain at ultra-high resolution”. X-ray diffraction, 2 ligands (GCP, CA), 12 pockets (best druggability 0.62). MolNFT v1 #32765 on GenesisL1: 3D structure…
- PDB
- 2C04
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein
- UniProt
- O07347
- Ligands
- GCP, CA
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein | protein | 297 | 52% helix, 13% strand | O07347 |
| B | Signal recognition particle protein | protein | 296 | 51% helix, 13% strand | O07347 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.62 | 0.78 | 26 | empty |
| 2 | 277 | 0.60 | 0.79 | 35 | empty |
| 3 | 165 | 0.50 | 0.77 | 16 | empty |
| 4 | 151 | 0.49 | 0.78 | 18 | empty |
| 5 | 128 | 0.46 | 0.78 | 31 | GCP |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2C04 · GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution · the same entry in another collection · chain A against A, TM-score 1.00
- O07347 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (O07347) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O07347
- Elsewhere: RCSB PDB 2C04 · PDBe 2C04 · UniProt O07347
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