4IVF | pdb_00004ivf

Crystal structure of glutathione transferase homolog from Lodderomyces elongisporus, target EFI-501753, with two GSH per subunit

PDB DOI: https://doi.org/10.2210/pdb4IVF/pdb

Classification: TRANSFERASE
Organism(s): Lodderomyces elongisporus NRRL YB-4239
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-22 Released: 2013-02-13
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.156 (Depositor), 0.159 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glutathione transferase homolog from Lodderomyces elongisporus, target EFI-501753, with two GSH per subunit

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 217.01 kDa
Atom Count: 16,087
Modeled Residue Count: 1,781
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H	231	Lodderomyces elongisporus NRRL YB-4239	Mutation(s): 0 Gene Names: LELG_04376
UniProt
Find proteins for A5E437 (Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239)) Explore A5E437 Go to UniProtKB: A5E437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5E437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], R [auth E], S [auth E], T [auth F], U [auth F], V [auth G], W [auth G], X [auth H], Y [auth H]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] MOL2 format, chain Q [auth E] mmCIF format, chain Q [auth E]	Q [auth E]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain Q [auth E] Interactions & Density Focus chain Q [auth E]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], R [auth E], S [auth E], T [auth F], U [auth F], V [auth G], W [auth G], X [auth H], Y [auth H]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.156 (Depositor), 0.159 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.598	α = 90
b = 112.476	β = 90
c = 194.384	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-13

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-02-13
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description