5NDX

The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I

PDB DOI: https://doi.org/10.2210/pdb5NDX/pdb

Classification: HYDROLASE
Organism(s): Rhizobium leguminosarum bv. trifolii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-03-09 Released: 2018-07-11
Deposition Author(s): Raich, L., Valero-Gonzalez, J., Castro-Lopez, J., Millan, C., Jimenez-Garcia, M.J., Nieto, P., Uson, I., Hurtado-Guerrero, R., Rovira, C.
Funding Organization(s): MICINN

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.175
R-Value Work: 0.159
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I.

Raich, L., Valero-Gonzalez, J., Castro-Lopez, J., Millan, C., Jimenez-Garcia, M.J., Nieto, P., Uson, I., Hurtado-Guerrero, R., Rovira, C.

To be published.

Macromolecule Content

Total Structure Weight: 70.64 kDa
Atom Count: 5,235
Modelled Residue Count: 606
Deposited Residue Count: 621
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase	A	621	Rhizobium leguminosarum bv. trifolii	Mutation(s): 2 Gene Names: BAE36_24485
UniProt
Find proteins for A0A1B8R7L2 (Rhizobium leguminosarum bv. trifolii) Explore A0A1B8R7L2 Go to UniProtKB: A0A1B8R7L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B8R7L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8U8 Query on 8U8 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	M [auth A], N [auth A]	(2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid C₁₆ H₁₆ O₉ ARQXEQLMMNGFDU-ZHMBSYLPSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]