SAXSdb — 3pus

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

PHD finger protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 5 CHLORIDE ION × 1 NICKEL (II) ION × 1 N-OXALYLGLYCINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 9 CHLORIDE ION × 1 NICKEL (II) ION × 1 N-OXALYLGLYCINE × 1 OXYGEN MOLECULE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 60–451 Author chain B； PDBConstruct 1–392； UniProt 60–451

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	3pus
Deposition date deposition_date	2010-12-06
Structure title title	PHF2 Jumonji-NOG-Ni(II)
Keywords keywords	alpha-ketoglutarate-Fe2+ dependent dioxygenases, PROTEIN BINDING; PROTEIN BINDING
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.

3pus__assembly_1__model_1

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

Download this curve (.dat)

3pus__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pus__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.03 Å
Rg (electron density)	20.98 Å
Total Rg	21.88 Å
Atom count	2889
Residues	365
Excluded volume	51413 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pus__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pus__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	PHD finger protein 2
Molecular weight formula_weight	44715.2 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	6036

STLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENASKAVRP

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

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3pusa_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.14 — Jumonji domain / Histone demethylase core

Domain ID domain_id	d3pusb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.14 — Jumonji domain / Histone demethylase core

CATH v4.4 (4 domains)

Domain ID domain_id	3pusA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	3pusA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1360 —

Domain ID domain_id	3pusB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	3pusB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1360 —

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Unit-cell length a length_a	65.353 Å
Unit-cell length b length_b	96.979 Å
Unit-cell length c length_c	66.194 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	33.530 Å
R factor r_factor	0.1774
R_work r_work	0.1751
R_free r_free	0.2318

PHF2 Jumonji-NOG-Ni(II)

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

PHD finger protein 2

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

3pus__assembly_1__model_1

3pus__assembly_1__model_1 | I(q)

3pus__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

PHF2 Jumonji-NOG-Ni(II)

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

PHD finger protein 2

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

3pus__assembly_1__model_1

3pus__assembly_1__model_1 | I(q)

3pus__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)