6NHS

Crystal Structure of the Beta Lactamase Class D YbXI from Nostoc

PDB DOI: https://doi.org/10.2210/pdb6NHS/pdb

Classification: HYDROLASE
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-23 Released: 2019-01-16
Deposition Author(s): Kim, Y., Tesar, C., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Beta Lactamase Class D YbXI from Nostoc

Kim, Y., Tesar, C., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 30.69 kDa
Atom Count: 2,160
Modelled Residue Count: 239
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	259	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Gene Names: all2480
UniProt
Find proteins for Q8YU74 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YU74 Go to UniProtKB: Q8YU74
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YU74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A]	D [auth A], E [auth A], F [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	C [auth A], G [auth A], I [auth A], J [auth A], K [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain B [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	B [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain B [auth A] Focus chain L [auth A] Focus chain M [auth A]