SAXSdb — 5h5s

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phospholipid hydroperoxide glutathione peroxidase, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GXpep-3 × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GPX4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 29–197

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5h5s
Deposition date deposition_date	2016-11-09
Structure title title	Crystal structure of human GPX4 in complex with GXpep-3
Keywords keywords	;PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE 4, SELENOCYSTEINE, OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex ;; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5h5s__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5h5s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h5s__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.57 Å
Rg (electron density)	15.19 Å
Total Rg	16.39 Å
Atom count	1447
Residues	177
Excluded volume	25835 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h5s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
Molecular weight formula_weight	19403.1 kDa
EC 编号 ec_number	1.11.1.12
Mutation mutation	C29S, C37A, C64S, U73C, C93R, C102S, C134E, C175V
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1577

SASRDDWRAARSMHEFSAKDIDGHMVNLDKYRGFVSIVTNVASQCGKTEVNYTQLVDLHARYAERGLRILAFPSNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKIEVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGVVVKRYGPMEEPLVIEKDLPHYF

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	GXpep-3
Molecular weight formula_weight	1561.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VPCPYLPLWNCAGK

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5h5sA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	35.017 Å
Unit-cell length b length_b	39.077 Å
Unit-cell length c length_c	59.394 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.84 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1682
R_work r_work	0.1663
R_free r_free	0.2038

Crystal structure of human GPX4 in complex with GXpep-3

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phospholipid hydroperoxide glutathione peroxidase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h5s__assembly_1__model_1

5h5s__assembly_1__model_1 | I(q)

5h5s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of human GPX4 in complex with GXpep-3

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phospholipid hydroperoxide glutathione peroxidase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h5s__assembly_1__model_1

5h5s__assembly_1__model_1 | I(q)

5h5s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)