MolNFT v1 · #167750 · protein

Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to 3'SLN

6VU6: “Sialic acid binding region of streptococcus sanguinis SK1 adhesin bound to 3'SLN”. X-ray diffraction, 4 ligands (NAG, GAL, SIA), 3 pockets (best druggability 0.54). MolNFT v1 #167750 on GenesisL1: 3D structure, binding sites and…

PDB: 6VU6
Type: protein
Length: 818 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adhesin
Ligands: NAG, GAL, SIA, CA
Pockets: 3 · best druggability 0.54

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

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · 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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.54	0.85	24	empty
2	95	0.35	0.74	21	empty
3	62	0.31	0.75	15	empty

Interfaces

1 interface between chains.

A–E · 586 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6VU6 · Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin bound to 3'sLn · 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 6VU6 · PDBe 6VU6

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