Research workbench
Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to sta
Analyse Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to sta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VT2
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adhesin
- Ligands
- A2G, GAL, SIA, CA, SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Adhesin | protein | 409 | 13% helix, 35% strand | — |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, E
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, E
- CA · Calcium ion · metal · 8 copies · chains A, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, E
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.49 | 0.84 | 21 | empty |
| 2 | 89 | 0.35 | 0.74 | 19 | empty |
| 3 | 76 | 0.32 | 0.74 | 17 | empty |
| 4 | 88 | 0.31 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–E · 576 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6VT2 · Sialic acid binding region of Streptococcus sanguinis SK1 adhesin bound to sTa · 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
- Elsewhere: RCSB PDB 6VT2 · PDBe 6VT2
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