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
- 4JDZ
- Type
- protein
- Length
- 875 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
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein sdrd | protein | 445 | 6% helix, 48% strand | E5QTK7 |
| A | Ser-asp rich FIBRINOGEN/BONE sialoprotein-binding protein sdrd | protein | 430 | 6% helix, 47% strand | E5QTK7 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.73 | 0.78 | 87 | CA |
| 2 | 653 | 0.68 | 0.77 | 72 | empty |
| 3 | 527 | 0.66 | 0.77 | 59 | empty |
| 4 | 124 | 0.47 | 0.79 | 24 | empty |
| 5 | 136 | 0.44 | 0.77 | 21 | CA |
Interfaces
1 interface between chains.
- B–A · 512 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4JDZ · Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the… · the same entry in another collection · chain B against B, 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 4JDZ · PDBe 4JDZ · UniProt E5QTK7
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