MolNFT v1 · #96240 · protein
Structures of sdrd from staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
4JDZ · 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), 6 pockets (best druggability…
- 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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