8iq0

Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state

Method: X-RAY DIFFRACTION

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

Superoxide dismutase [Cu-Zn]

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 GLYCEROL × 1 SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 SULFATE ION × 1 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 SULFATE ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 1,2-ETHANEDIOL × 1 HYDROSULFURIC ACID × 1 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODC_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 2–152 Author chain B； PDBConstruct 1–151； UniProt 2–152 Author chain C； PDBConstruct 1–151； UniProt 2–152 Author chain D； PDBConstruct 1–151； UniProt 2–152 Author chain E； PDBConstruct 1–151； UniProt 2–152 Author chain F； PDBConstruct 1–151； UniProt 2–152 Author chain G； PDBConstruct 1–151； UniProt 2–152 Author chain H； PDBConstruct 1–151； UniProt 2–152 Author chain I； PDBConstruct 1–151； UniProt 2–152 Author chain J； PDBConstruct 1–151； UniProt 2–152 Author chain K； PDBConstruct 1–151； UniProt 2–152 Author chain L； PDBConstruct 1–151； UniProt 2–152 Author chain M； PDBConstruct 1–151； UniProt 2–152 Author chain N； PDBConstruct 1–151； UniProt 2–152 Author chain O； PDBConstruct 1–151； UniProt 2–152 Author chain P； PDBConstruct 1–151； UniProt 2–152

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	8iq0
Deposition date deposition_date	2023-03-15
Structure title title	Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state
Keywords keywords	dimer, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

8iq0__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8iq0__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8iq0__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	20.78 Å
Rg (electron density)	19.89 Å
Total Rg	20.62 Å
Atom count	2185
Residues	302
Excluded volume	38322 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8iq0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8iq0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8iq0__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8iq0__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`8iq0__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`8iq0__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`8iq0__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`8iq0__assembly_8__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 (9)

Entity 1 Entity 1 polymer

Description description	Superoxide dismutase [Cu-Zn]
Molecular weight formula_weight	15573.3 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	18883

ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1643

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	8iq0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0M01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0N01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0O01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0P01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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Unit-cell length a length_a	74.348 Å
Unit-cell length b length_b	91.474 Å
Unit-cell length c length_c	91.164 Å
Unit-cell angle α angle_alpha	85.00 °
Unit-cell angle β angle_beta	78.06 °
Unit-cell angle γ angle_gamma	66.76 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	30.680 Å
R factor r_factor	0.2031
R_work r_work	0.2009
R_free r_free	0.2445

Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state

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

Superoxide dismutase [Cu-Zn]

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

8iq0__assembly_3__model_1

8iq0__assembly_3__model_1 | I(q)

8iq0__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state

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

Superoxide dismutase [Cu-Zn]

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

8iq0__assembly_3__model_1

8iq0__assembly_3__model_1 | I(q)

8iq0__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)