8WXD | pdb_00008wxd

Crystal Structure of shaft pilin PilA from Streptococcus sanguinis

PDB DOI: https://doi.org/10.2210/pdb8WXD/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Streptococcus sanguinis SK36
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-28 Released: 2025-05-07
Deposition Author(s): Yadav, S., Parijat, P., Krishnan, V.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.259 (Depositor), 0.263 (DCC)
R-Value Work:
0.209 (Depositor), 0.216 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of shaft pilin PilA from Streptococcus sanguinis

Yadav, S., Parijat, P., Krishnan, V.

To be published.

Macromolecule Content

Total Structure Weight: 98.81 kDa
Atom Count: 6,499
Modeled Residue Count: 838
Deposited Residue Count: 902
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein, putative	A, B	451	Streptococcus sanguinis SK36	Mutation(s): 0 Gene Names: SSA_1632
UniProt
Find proteins for A3CPB5 (Streptococcus sanguinis (strain SK36)) Explore A3CPB5 Go to UniProtKB: A3CPB5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3CPB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD (Subject of Investigation/LOI) Query on CD Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] P [auth B] Q [auth B] I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A]	G [auth A], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] M [auth B] C [auth A], D [auth A], E [auth A], F [auth A], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B]