SAXSdb — 1okg

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

POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE

LEISHMANIA MAJOR

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 SULFITE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9NE49
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 1–370

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	1okg
Deposition date deposition_date	2003-07-24
Structure title title	3-mercaptopyruvate sulfurtransferase from Leishmania major
Keywords keywords	;MERCAPTOPYRUVATE, SULFURTRANSFERASE, RHODANESE, PROLYL ISOMERASE, CATALYTIC TRIAD, SERINE PROTEASE, LEISHMANIA PYRUVATE, TRANSFERASE ;; TRANSFERASE
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.

1okg__assembly_1__model_1

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

Download this curve (.dat)

1okg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1okg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.09 Å
Rg (electron density)	22.49 Å
Total Rg	23.25 Å
Atom count	2783
Residues	347
Excluded volume	49439 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1okg__assembly_1__model_1`	monomeric （1）	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	POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
Molecular weight formula_weight	41297.7 kDa
EC 编号 ec_number	2.8.1.2
Mutation mutation	YES
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	3193

MSAPAAAPKHPGKVFLDPSEVADHLAEYRIVDCRYSLKIKDHGSIQYAKEHVKSAIRADVDTNLSKLVPTSTARHPLPPCAEFIDWCMANGMAGELPVLCYDDECGAMGGCRLWWMLNSLGADAYVINGGFQACKAAGLEMESGEPSSLPRPATHWPFKTAFQHHYLVDEIPPQAIITDARSADRFASTVRPYAADKMPGHIEGARNLPYTSHLVTRGDGKVLRSEEEIRHNIMTVVQGAGDAADLSSFVFSCGSGVTACINIALVHHLGLGHPYLYCGSWSEYSGLFRPPIMRSIIDDYGMCMQMQTPSLGDNPKANLDTMTLKVDGAPCERPDAEVQSAATHLHAGEAATVYFKSGRVVTIEVPVVPNLEA

Source Source

Source organism organism	LEISHMANIA MAJOR
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFITE ION
Molecular weight formula_weight	80.1 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	404

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1okga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamily	c.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family family	c.46.1.2 — Multidomain sulfurtransferase (rhodanese)

Domain ID domain_id	d1okga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamily	c.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family family	c.46.1.2 — Multidomain sulfurtransferase (rhodanese)

Domain ID domain_id	d1okga3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.3 — 3-mercaptopyruvate sulfurtransferase, C-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1okgA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	1okgA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

Domain ID domain_id	1okgA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1670 — 3-mercaptopyruvate sulfurtransferase, domain 3
Homologous superfamily homologous superfamily	10 — 3-mercaptopyruvate sulfurtransferase, domain 3

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Unit-cell length a length_a	109.574 Å
Unit-cell length b length_b	109.574 Å
Unit-cell length c length_c	67.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	76.700 Å
R factor r_factor	0.2120
R_work r_work	0.2080
R_free r_free	0.2870

3-mercaptopyruvate sulfurtransferase from Leishmania major

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

POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE

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

1okg__assembly_1__model_1

1okg__assembly_1__model_1 | I(q)

1okg__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

3-mercaptopyruvate sulfurtransferase from Leishmania major

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

POSSIBLE 3-MERCAPTOPYRUVATE SULFURTRANSFERASE

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

1okg__assembly_1__model_1

1okg__assembly_1__model_1 | I(q)

1okg__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)