Research workbench
Gmppnp complex of srp GTPase ng domain
Analyse Gmppnp complex of srp GTPase ng domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JPN
- Type
- protein
- Length
- 591 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein
- UniProt
- O07347
- Ligands
- GNP, CA
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Signal recognition particle protein | protein | 295 | 50% helix, 13% strand | O07347 |
| A | Signal recognition particle protein | protein | 296 | 51% helix, 13% strand | O07347 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- ACY · Acetic acid · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.66 | 0.79 | 35 | empty |
| 2 | 163 | 0.56 | 0.81 | 23 | empty |
| 3 | 198 | 0.52 | 0.77 | 34 | empty |
| 4 | 142 | 0.47 | 0.77 | 16 | ACY |
| 5 | 73 | 0.44 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 595 Ų buried · 4 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 1JPN · PDBe 1JPN · UniProt O07347
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