MolNFT v1 · #118040 · protein
Crystal structure of the srpa adhesin from streptococcus sanguinis with a sialyl galactose disaccharide bound
5EQ3 · Platelet-binding glycoprotein: “Crystal structure of the srpa adhesin from streptococcus sanguinis with a sialyl galactose disaccharide bound”. X-ray diffraction, 4 ligands (MBG, NGC, CA), 1 pocket (best druggability 0.26). MolNFT…
- PDB
- 5EQ3
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-binding glycoprotein
- UniProt
- A3CM52
- Ligands
- MBG, NGC, CA, NA
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-binding glycoprotein | protein | 198 | 12% helix, 36% strand | A3CM52 |
| B | Platelet-binding glycoprotein | protein | 194 | 12% helix, 35% strand | A3CM52 |
Ligands and binding sites
- MBG · methyl beta-D-galactopyranoside · ligand · chains A
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · chains A
- CA · Calcium ion · metal · 7 copies · chains A, B
- NA · Sodium ion · metal · chains B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.26 | 0.73 | 19 | ACT |
Interfaces
1 interface between chains.
- A–B · 567 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5EQ3 · Crystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl… · 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 A3CM52
- Elsewhere: RCSB PDB 5EQ3 · PDBe 5EQ3 · UniProt A3CM52
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