SAXSdb — 5fdz

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

Histone acetyltransferase KAT2B

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	~{N}-methyl-2-(oxan-4-yloxy)-5-(2-oxidanylidene-2-phenylazanyl-ethoxy)benzamide × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAT2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–119； UniProt 715–831 Author chain B； PDBConstruct 3–119； UniProt 715–831

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	5fdz
Deposition date deposition_date	2015-12-16
Structure title title	Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a (compound 14)
Keywords keywords	;SIGNALING PROTEIN, bromodomain, Histone acetyltransferase KAT2B, histone, acetylation, acetyllysine, epigenetics, structural genomics consortium (SGC) ;; SIGNALING 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.

5fdz__assembly_1__model_1

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

Download this curve (.dat)

5fdz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fdz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.88 Å
Rg (electron density)	17.78 Å
Total Rg	18.83 Å
Atom count	1834
Residues	213
Excluded volume	33034 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fdz__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 (4)

Entity 1 Entity 1 polymer

Description description	Histone acetyltransferase KAT2B
Molecular weight formula_weight	14172.4 kDa
EC 编号 ec_number	2.3.1.48
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	1919

SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID

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	~{N}-methyl-2-(oxan-4-yloxy)-5-(2-oxidanylidene-2-phenylazanyl-ethoxy)benzamide
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5fdza_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

Domain ID domain_id	d5fdzb_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.1 — Bromodomain

CATH v4.4 (2 domains)

Domain ID domain_id	5fdzA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	5fdzB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	99.770 Å
Unit-cell length b length_b	99.770 Å
Unit-cell length c length_c	100.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.860 Å
R factor r_factor	0.2139
R_work r_work	0.2124
R_free r_free	0.2439

Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a (compound 14)

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

Histone acetyltransferase KAT2B

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

5fdz__assembly_1__model_1

5fdz__assembly_1__model_1 | I(q)

5fdz__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of human PCAF bromodomain in complex with compound BDOMB00091a (compound 14)

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

Histone acetyltransferase KAT2B

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

5fdz__assembly_1__model_1

5fdz__assembly_1__model_1 | I(q)

5fdz__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)