SAXSdb — 2puy

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

PHD finger protein 21A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Histone H3 × 1 （P61836） ZINC ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PF21A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–60； UniProt 486–543 Author chain B； PDBConstruct 3–60； UniProt 486–543

Histone H3

OrganismNot specified

UniProt P61836

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PHD finger protein 21A × 2 （Q96BD5） ZINC ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_ZYGBA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–10； UniProt 2–11

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	2puy
Deposition date deposition_date	2007-05-09
Structure title title	Crystal Structure of the BHC80 PHD finger
Keywords keywords	PHD finger, Histone code, BRAF-HDAC complex, TRANSCRIPTION; TRANSCRIPTION
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.

2puy__assembly_1__model_1

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

Download this curve (.dat)

2puy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2puy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.94 Å
Rg (electron density)	16.09 Å
Total Rg	16.98 Å
Atom count	1022
Residues	129
Excluded volume	18363 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2puy__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	PHD finger protein 21A
Molecular weight formula_weight	7007.4 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	1166

HMIHEDFCSVCRKSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEEAI

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

Entity 2 Entity 2 polymer

Description description	Histone H3
Molecular weight formula_weight	1150.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

ARTKQTARKS

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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2puya1
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.0 — automated matches

Domain ID domain_id	d2puya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2puyb1
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.0 — automated matches

Domain ID domain_id	d2puyb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2puyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	2puyB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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Unit-cell length a length_a	79.511 Å
Unit-cell length b length_b	25.386 Å
Unit-cell length c length_c	62.282 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.430 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2310

Crystal Structure of the BHC80 PHD finger

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

PHD finger protein 21A

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3

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

2puy__assembly_1__model_1

2puy__assembly_1__model_1 | I(q)

2puy__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the BHC80 PHD finger

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

PHD finger protein 21A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3

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

2puy__assembly_1__model_1

2puy__assembly_1__model_1 | I(q)

2puy__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)