9Q3H | pdb_00009q3h

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

PDB DOI: https://doi.org/10.2210/pdb9Q3H/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Streptococcus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-18 Released: 2025-09-10
Deposition Author(s): Morrison, K.M., Martin, K.A., Iverson, T.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

Morrison, K.M., Martin, K.A., Iverson, T.M.

To be published.

Macromolecule Content

Total Structure Weight: 30.25 kDa
Atom Count: 2,236
Modeled Residue Count: 247
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet binding protein GspB	A, B	127	Streptococcus	Mutation(s): 0 Gene Names: gspB
UniProt
Find proteins for A8AWU7 (Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)) Explore A8AWU7 Go to UniProtKB: A8AWU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8AWU7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	C, D	3		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G65562ZE GlyCosmos: G65562ZE GlyGen: G65562ZE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VP1 (Subject of Investigation/LOI) Query on VP1 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	Fluorenylmethyloxycarbonyl chloride C₁₅ H₁₁ Cl O₂ IRXSLJNXXZKURP-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
SER (Subject of Investigation/LOI) Query on SER Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]