SAXSdb — 2qd0

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

Zinc finger CDGSH domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZCD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–79； UniProt 32–108 Author chain B； PDBConstruct 3–79； UniProt 32–108

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	2qd0
Deposition date deposition_date	2007-06-20
Structure title title	Crystal structure of mitoNEET
Keywords keywords	iron-sulfur cluster, [2FE-2S], HISTIDINE LIGATION, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

2qd0__assembly_1__model_1

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

Download this curve (.dat)

2qd0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qd0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.65 Å
Rg (electron density)	14.62 Å
Total Rg	15.58 Å
Atom count	1082
Residues	133
Excluded volume	19260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qd0__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 (3)

Entity 1 Entity 1 polymer

Description description	Zinc finger CDGSH domain-containing protein 1
Molecular weight formula_weight	9379.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1223

GSKRFYVKDHRNKAMINLHIQKDNPKIVHAFDMEDLGDKAVYCRCWRSKKFPFCDGAHTKHNEETGDNVGPLIIKKKETAS

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qd0a_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d2qd0b_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

CATH v4.4 (2 domains)

Domain ID domain_id	2qd0A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	2qd0B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

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Unit-cell length a length_a	43.838 Å
Unit-cell length b length_b	59.139 Å
Unit-cell length c length_c	65.971 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	21.920 Å
R factor r_factor	0.1660
R_work r_work	0.1640
R_free r_free	0.1930

Crystal structure of mitoNEET

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

Zinc finger CDGSH domain-containing protein 1

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

2qd0__assembly_1__model_1

2qd0__assembly_1__model_1 | I(q)

2qd0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of mitoNEET

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

Zinc finger CDGSH domain-containing protein 1

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

2qd0__assembly_1__model_1

2qd0__assembly_1__model_1 | I(q)

2qd0__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)