6XT1 | pdb_00006xt1

The structure of the M60 catalytic domain from Clostridium perfringens ZmpC in complex the sialyl T antigen

PDB DOI: https://doi.org/10.2210/pdb6XT1/pdb

Classification: HYDROLASE
Organism(s): Clostridium perfringens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-16 Released: 2021-02-03
Deposition Author(s): Pluvinage, B., Boraston, A.B.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Canadian Glycomics Network (GLYCONET)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Molecular insights into architecturally complex glycopeptidases

Pluvinage, B., Ficko-Blean, E., Noach, I., Stuart, C., Thompson, N., McClure, H., Buenbrazo, N., Wakarchuck, W., Boraston, A.B.

(2021) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 243.77 kDa
Atom Count: 16,813
Modeled Residue Count: 2,038
Deposited Residue Count: 2,124
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZmpC Glycopeptidase	A, B, C, D	531	Clostridium perfringens	Mutation(s): 0 Gene Names: CP4_3468
UniProt
Find proteins for F8UNJ8 (Clostridium perfringens) Explore F8UNJ8 Go to UniProtKB: F8UNJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8UNJ8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose	E [auth F], F [auth M]	3		O-Glycosylation	Interactions Focus chain E [auth F] Focus chain F [auth M] Interactions & Density Focus chain E [auth F] Focus chain F [auth M]
Glycosylation Resources
GlyTouCan: G56682BC GlyCosmos: G56682BC GlyGen: G56682BC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	J [auth A], P [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain X [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain X [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], Q [auth C], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] H [auth A] I [auth A] L [auth B] AA [auth D], BA [auth D], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]