MolNFT v1 · #96241 · protein
Structures of sdrd from staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
4JE0 · Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein…: “Structures of sdrd from staphylococcus aureus reveal the molecular mechanism of how the cell surface…”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability…
- 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
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