6UBV | pdb_00006ubv

The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin

PDB DOI: https://doi.org/10.2210/pdb6UBV/pdb

Classification: CELL ADHESION
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-13 Released: 2020-09-16
Deposition Author(s): Schormann, N., Deivanayagam, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin

Schormann, N., Deivanayagam, C.

To be published.

Macromolecule Content

Total Structure Weight: 188.7 kDa
Atom Count: 12,619
Modeled Residue Count: 1,573
Deposited Residue Count: 1,700
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein adhesin	A, B, C, D	425	Streptococcus mutans	Mutation(s): 0 Gene Names: spaP
UniProt
Find proteins for P11657 (Streptococcus mutans) Explore P11657 Go to UniProtKB: P11657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11657
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SNZ (Subject of Investigation/LOI) Query on SNZ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	F [auth A], I [auth B], M [auth C], R [auth D]	N-(3,4-dihydroxyphenyl)-N'-[2-(3,4-dihydroxyphenyl)ethyl]urea C₁₅ H₁₆ N₂ O₅ XPAUTCCLOUPUGJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	J [auth B], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain K [auth B]	K [auth B], O [auth C], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], L [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	G [auth A], N [auth C], S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth D]