MolNFT v1 · #17167 · protein
Homo-heterodimeric complex of the srp gtpases
1OKK · Signal recognition particle protein: “Homo-heterodimeric complex of the srp gtpases”. X-ray diffraction, 4 ligands (GCP, BZP, MG), 8 pockets (best druggability 0.82). MolNFT v1 #17167 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1OKK
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein; Cell division protein ftsy
- UniProt
- O07347, P83749
- Ligands
- GCP, BZP, MG, SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle protein | protein | 290 | 50% helix, 14% strand | O07347 |
| D | Cell division protein ftsy | protein | 265 | 47% helix, 14% strand | P83749 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, D
- BZP · N1-carboxypiperazine · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.82 | 0.88 | 77 | GCP, MG |
| 2 | 51 | 0.70 | 0.98 | 23 | EDO |
| 3 | 102 | 0.53 | 0.83 | 20 | empty |
| 4 | 163 | 0.46 | 0.76 | 26 | empty |
| 5 | 77 | 0.39 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–D · 1614 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1OKK · Homo-heterodimeric complex of the srp gtpases · the same entry in another collection · chain A against A, TM-score 1.00
- P83749 · AlphaFold monomer V2.0 prediction for signal recognition particle receptor ftsy (P83749) · a predicted model of the same protein · chain D against A, TM-score 0.96
- O07347 · AlphaFold monomer V2.0 prediction for signal recognition particle protein (O07347) · a predicted model of the same protein · chain A against A, TM-score 0.92
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
- Every structure of UniProt P83749
- Elsewhere: RCSB PDB 1OKK · PDBe 1OKK · UniProt O07347 · UniProt P83749
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