MolNFT v1 · #167712 · protein
Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to sta
6VT2: “Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to sta”. X-ray diffraction, 5 ligands (A2G, GAL, SIA), 4 pockets (best druggability 0.49). MolNFT v1 #167712 on GenesisL1: 3D structure, binding sites and…
- 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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