5EIG | pdb_00005eig

Engineered human cystathionine gamma lyase (E59T, E339V) to deplet cysteine

PDB DOI: https://doi.org/10.2210/pdb5EIG/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-10-29 Released: 2016-11-09
Deposition Author(s): Yan, W., Zhang, J.
Funding Organization(s): University of Texas at Austin Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Systemic Depletion of Serum L-Cyst(e)ine with an Engineered Human Enzyme Mediates Potent Induction of ROS and Cancer Ablation

Cramer, S., Saha, A., Tadi, S., Tiziani, S., Yan, W., Triplett, K., Lamb, C., Alters, S., Johnson, D., Zhang, Y., DiGiovanni, J., Georgiou, G., Stone, E.

To be published.

Macromolecule Content

Total Structure Weight: 359.41 kDa
Atom Count: 24,750
Modeled Residue Count: 3,087
Deposited Residue Count: 3,240
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase	A, C, D, E, F A, C, D, E, F, G	405	Homo sapiens	Mutation(s): 2 Gene Names: CTH EC: 4.4.1.1 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens) Explore P32929 Go to UniProtKB: P32929
PHAROS: P32929 GTEx: ENSG00000116761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32929
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase	B, H	405	Homo sapiens	Mutation(s): 2 Gene Names: CTH EC: 4.4.1.1 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P32929 (Homo sapiens) Explore P32929 Go to UniProtKB: P32929
PHAROS: P32929 GTEx: ENSG00000116761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32929
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain O [auth G] SDF format, chain M [auth E] MOL2 format, chain K [auth C] MOL2 format, chain O [auth G] MOL2 format, chain M [auth E] mmCIF format, chain K [auth C] mmCIF format, chain O [auth G] mmCIF format, chain M [auth E]	K [auth C], M [auth E], O [auth G]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain N [auth F] SDF format, chain L [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain P [auth H] MOL2 format, chain N [auth F] MOL2 format, chain L [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain P [auth H] mmCIF format, chain N [auth F] mmCIF format, chain L [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], L [auth D], N [auth F], P [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5OW Query on 5OW	A, C, D, E, F A, C, D, E, F, G	L-PEPTIDE LINKING	C₁₇ H₂₇ N₄ O₉ P S		LYS
LLP Query on LLP	B, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.191 (Depositor), 0.193 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.377	α = 90
b = 163.455	β = 90
c = 181.625	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Yan, W.

Zhang, J.

Funding Organization	Location	Grant Number
University of Texas at Austin Welch Foundation	United States	F-1778

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2025-04-02
Changes: Data collection, Database references, Derived calculations, Structure summary