21KB | pdb_000021kb

Cystathionine beta-lyase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb21KB/pdb

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


• Deposited: 2025-12-15 Released: 2026-02-11 
• Deposition Author(s): Varfolomeeva, L.A., Anufrieva, N.V., Morozova, E.A., Puchkov, V.M., Kulikova, V.V., Revtovich, S.V., Minyaev, M.E., Popov, V.O., Solyev, P.N., Boyko, K.M.
• Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: in silico

Literature

Klebsiella pneumoniae cystathionine beta-lyase-structure-functional analysis of a promising component of the enzyme-prodrug binary system

Anufrieva, N.V., Morozova, E.A., Puchkov, V.M., Tkachev, Y.V., Kulikova, V.V., Revtovich, S.V., Mitkevich, V.A., Makarov, A.A., Minyaev, M.E., Varfolomeeva, L.A., Popov, V.O., Boyko, K.M., Solyev, P.N.

(2026) Mol Catal 592: 115767

• DOI: https://doi.org/10.1016/j.mcat.2026.115767

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 174.42 kDa 
• Atom Count: 13,722 
• Modeled Residue Count: 1,565 
• Deposited Residue Count: 1,580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine-S-conjugate beta-lyase	A, B, C, D	395	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  metC, metC_1, metC_2, metC_4, B5L96_16180, B6I68_11540, BANRA_02509, BL124_00018915, CP554_04135, DM078_01535, DW286_17480, E1814_21630, EAO17_10070, FXN67_07235, G4V31_19190, GJJ01_08005, GJJ08_003585, GNF00_15520, H3G96_024120, JMZ77_03585, LS45_25460, NCTC11679_00773, NCTC13443_06402, NCTC204_02949, NCTC5051_04552, NCTC5052_04013, NCTC5053_05113, NCTC8849_05374, NCTC9601_00031, NCTC9637_01279, Q6294_05520, SAMEA104567804_01826, SAMEA3499874_00682, SAMEA3499901_04217, SAMEA3515122_03450, SAMEA3538828_04005, SAMEA3649591_00131, SAMEA3649733_03630, SAMEA3720909_03545, SAMEA3729652_02328, SAMEA4873632_04081 EC: 4.4.1.13
UniProt
Find proteins for Q0ZBA0 (Klebsiella pneumoniae) Explore Q0ZBA0  Go to UniProtKB:  Q0ZBA0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	G [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	E [auth A], F [auth B], H [auth C], I [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.418	α = 90
b = 131.209	β = 100.46
c = 84.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Varfolomeeva, L.A., Anufrieva, N.V., Morozova, E.A., Puchkov, V.M., Kulikova, V.V., Revtovich, S.V., Minyaev, M.E., Popov, V.O., Solyev, P.N., Boyko, K.M.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2025-454

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release