Research workbench
Structures of sdrd from staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
Analyse Structures of sdrd from staphylococcus aureus reveal the molecular mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JE0
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein sdrd
- UniProt
- E5QTK7
- Ligands
- CA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein sdrd | protein | 311 | 8% helix, 49% strand | E5QTK7 |
| B | Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein sdrd | protein | 313 | 6% helix, 50% strand | E5QTK7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.69 | 0.77 | 66 | empty |
| 2 | 494 | 0.65 | 0.77 | 63 | empty |
| 3 | 432 | 0.64 | 0.78 | 57 | empty |
| 4 | 85 | 0.39 | 0.78 | 14 | empty |
| 5 | 53 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4JE0 · Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the… · the same entry in another collection · chain A against A, TM-score 1.00
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 E5QTK7
- Elsewhere: RCSB PDB 4JE0 · PDBe 4JE0 · UniProt E5QTK7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.