8DUY | pdb_00008duy

Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8DUY/pdb

Classification: LYASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-27 Released: 2022-08-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.195 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Cystathionine beta-lyase from Klebsiella pneumoniae

Dranow, D.M., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 178.64 kDa
Atom Count: 14,023
Modeled Residue Count: 1,566
Deposited Residue Count: 1,612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase	A, B, C, D	403	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: KPHS_45550 EC: 4.4.1.8 (PDB Primary Data), 4.4.1.13 (UniProt)
UniProt
Find proteins for A0A0H3GVN6 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GVN6 Go to UniProtKB: A0A0H3GVN6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GVN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A]	G [auth A], L [auth C], O [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth C] E [auth A], F [auth A], H [auth B], I [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]