Research workbench
Water structure of T. aquaticus ffh ng domain at 1.1A resolution
Analyse Water structure of T. aquaticus ffh ng domain at 1.1A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J45
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle protein
- UniProt
- O07347
- Ligands
- CA, NA
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Signal recognition particle protein | protein | 297 | 53% helix, 13% strand | O07347 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.67 | 0.79 | 37 | EDO |
| 2 | 144 | 0.51 | 0.80 | 22 | empty |
| 3 | 64 | 0.50 | 0.85 | 16 | empty |
| 4 | 157 | 0.50 | 0.78 | 34 | empty |
| 5 | 77 | 0.46 | 0.81 | 12 | MRD |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2J45 · Water structure of T. Aquaticus Ffh NG Domain At 1.1A 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 A against A, TM-score 0.98
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 2J45 · PDBe 2J45 · UniProt O07347
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