MolNFT v1 · #16747 · protein
A new mggdp complex of the ffh ng domain
1O87 · Signal recognition particle protein: “A new mggdp complex of the ffh ng domain”. X-ray diffraction, 3 ligands (GDP, MG, CL), 10 pockets (best druggability 0.58). MolNFT v1 #16747 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1O87
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein
- UniProt
- O07347
- Ligands
- GDP, MG, CL
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Signal recognition particle protein | protein | 295 | 52% helix, 13% strand | O07347 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.58 | 0.83 | 29 | FMT |
| 2 | 58 | 0.56 | 0.89 | 17 | empty |
| 3 | 111 | 0.56 | 0.84 | 23 | empty |
| 4 | 108 | 0.43 | 0.78 | 22 | empty |
| 5 | 78 | 0.41 | 0.78 | 16 | FMT |
Interfaces
1 interface between chains.
- A–B · 1387 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 1O87 · PDBe 1O87 · UniProt O07347
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