SAXSdb — 4o64

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

Lysine-specific demethylase 2B

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	ZINC ION × 4 UNKNOWN ATOM OR ION × 6 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 4 UNKNOWN ATOM OR ION × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 4 UNKNOWN ATOM OR ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–118； UniProt 607–723 Author chain B； PDBConstruct 2–118； UniProt 607–723 Author chain C； PDBConstruct 2–118； UniProt 607–723

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	4o64
Deposition date deposition_date	2013-12-20
Structure title title	Zinc fingers of KDM2B
Keywords keywords	CXXC zinc finger, ring zinc finger, Structural Genomics, Structural Genomics Consortium, SGC, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4o64__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`4o64__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3	1	`4o64__assembly_3__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	Lysine-specific demethylase 2B
Molecular weight formula_weight	13350.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2791

GRRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCN

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4o64A01
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	4o64B01
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	4o64C01
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	107.322 Å
Unit-cell length b length_b	107.322 Å
Unit-cell length c length_c	34.130 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	9

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1914
R_work r_work	0.1905
R_free r_free	0.2198

Zinc fingers of KDM2B

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

Lysine-specific demethylase 2B

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

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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Zinc fingers of KDM2B

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

Lysine-specific demethylase 2B

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

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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)