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5w1f

Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein S100-A8

Homo sapiens

UniProt P05109

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Protein S100-A9 × 2 （P06702） SODIUM ION × 3 CALCIUM ION × 5 NICKEL (II) ION × 3 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Protein S100-A9 × 2 （P06702） SODIUM ION × 3 CALCIUM ION × 5 NICKEL (II) ION × 3 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1mr8 5hlo 5hlo 5hlv 5hlv 5hlv 5hlv

7 assemblies

Homotetramer
1mr8

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1xk4 1xk4 1xk4 4ggf 4ggf 4xjk 4xjk 4xjk 5w1f 5w1f 6ds2 6ds2

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name S10A8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–93； UniProt 1–93 Author chain C； PDBConstruct 1–93； UniProt 1–93 Author chain E； PDBConstruct 1–93； UniProt 1–93 Author chain G； PDBConstruct 1–93； UniProt 1–93

Protein S100-A9

Homo sapiens

UniProt P06702

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Protein S100-A8 × 2 （P05109） SODIUM ION × 3 CALCIUM ION × 5 NICKEL (II) ION × 3 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Protein S100-A8 × 2 （P05109） SODIUM ION × 3 CALCIUM ION × 5 NICKEL (II) ION × 3 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1irj 1irj 1irj 1irj 5i8n 7ui5

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1xk4 1xk4 1xk4 4ggf 4ggf 4xjk 4xjk 4xjk 5w1f 5w1f 6ds2 6ds2

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name S10A9_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–114； UniProt 1–114 Author chain D； PDBConstruct 1–114； UniProt 1–114 Author chain F； PDBConstruct 1–114； UniProt 1–114 Author chain H； PDBConstruct 1–114； UniProt 1–114

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_id5w1f
Deposition date deposition_date2017-06-03
Structure title titleCrystal structure of Ni(II)- and Ca(II)-bound human calprotectin
Keywords keywordscalprotectin, innate immunity, metal sequestration, nickel, calcium, S100 protein, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-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.

5w1f__assembly_1__model_1

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

Download this curve (.dat)

5w1f__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5w1f__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）21.82 Å
Rg (electron density)20.59 Å
Total Rg21.54 Å
Atom count3204
Residues390
Excluded volume57350 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5w1f__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5w1f__assembly_2__model_1 tetrameric （4） 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 (6)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5w1fa_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fb_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fc_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fd_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fe_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1ff_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fg_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd5w1fh_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins

CATH v4.4 (8 domains)

Domain ID domain_id5w1fA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id5w1fH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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7. Citations (1)