8PN3

Crystal structure of the HC7-Glu200Ala mutant complexed to a tetraglycopeptide.

PDB DOI: https://doi.org/10.2210/pdb8PN3/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-03-06
Deposition Author(s): Taleb, V., Hurtado-Guerrero, R.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.201
R-Value Work: 0.170
R-Value Observed: 0.171

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

A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases

Narimatsu, Y., Bull, C., Taleb, V., Liao, Q., Companon, I., Sanchez-Navarro, D., Durbesson, F., Vincentelli, R., Hansen, L., Corzana, F., Rovira, C., Henrissat, B., Clausen, H., Joshi, H.J., Hurtado-Guerrero, R.

(2024) Nat Catal

DOI: https://doi.org/10.1038/s41929-024-01116-5

Macromolecule Content

Total Structure Weight: 153.07 kDa
Atom Count: 6,600
Modelled Residue Count: 706
Deposited Residue Count: 1,348
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3472 domain-containing protein	A, B	659	Bacillus cereus	Mutation(s): 0 Gene Names: DN401_14795
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetraglycopeptide	C, D	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G (Subject of Investigation/LOI) Query on A2G Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain J [auth C] SDF format, chain M [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth C] MOL2 format, chain M [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth C] mmCIF format, chain M [auth C]	J [auth C] K [auth C] L [auth C] M [auth C] N [auth D] J [auth C], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D], Q [auth D]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]