← Back to search
1q0d

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state

Method: X-RAY DIFFRACTION
▼

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

Superoxide dismutase [Ni]

OrganismNot specified

UniProt P80734

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 SULFATE ION × 8 NICKEL (III) ION × 6 water × 6 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 6 SULFATE ION × 8 NICKEL (III) ION × 6 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
1q0d 1q0d 1q0f 1q0f 1q0g 1q0g 1q0k 1q0k 1q0m

9 assemblies

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name SODN_STRSO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–117； UniProt 15–131 Author chain B； PDBConstruct 1–117； UniProt 15–131 Author chain C； PDBConstruct 1–117； UniProt 15–131 Author chain D； PDBConstruct 1–117； UniProt 15–131 Author chain E； PDBConstruct 1–117； UniProt 15–131 Author chain F； PDBConstruct 1–117； UniProt 15–131 Author chain G； PDBConstruct 1–117； UniProt 15–131 Author chain H； PDBConstruct 1–117； UniProt 15–131 Author chain I； PDBConstruct 1–117； UniProt 15–131 Author chain J； PDBConstruct 1–117； UniProt 15–131 Author chain K； PDBConstruct 1–117； UniProt 15–131 Author chain L； PDBConstruct 1–117； UniProt 15–131

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1q0d
Deposition date deposition_date2003-07-16
Structure title titleCrystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state
Keywords keywordsHOMOHEXAMER OF FOUR-HELIX BUNDLES, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

1q0d__assembly_1__model_1

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

Download this curve (.dat)

1q0d__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1q0d__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）25.60 Å
Rg (electron density)24.73 Å
Total Rg25.45 Å
Atom count5632
Residues702
Excluded volume99860 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1q0d__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1q0d__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1q0da_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0db_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dc_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dd_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0de_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0df_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dg_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dh_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0di_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dj_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dk_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD
Domain ID domain_idd1q0dl_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family familya.24.22.1 — Nickel-containing superoxide dismutase, NiSOD

CATH v4.4 (12 domains)

Domain ID domain_id1q0dA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dE00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dH00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dI00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dK00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
Domain ID domain_id1q0dL00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily400 — Nickel-containing superoxide dismutase
▶

7. Citations (1)