3bbf

Crystal structure of the NM23-H2 transcription factor complex with GDP

Method: X-RAY DIFFRACTION

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

Nucleoside diphosphate kinase B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GUANOSINE-5'-DIPHOSPHATE × 6 MAGNESIUM ION × 6 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDKB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 2–152 Author chain B； PDBConstruct 1–151； UniProt 2–152 Author chain C； PDBConstruct 1–151； UniProt 2–152 Author chain D； PDBConstruct 1–151； UniProt 2–152 Author chain E； PDBConstruct 1–151； UniProt 2–152 Author chain F； PDBConstruct 1–151； UniProt 2–152

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	3bbf
Deposition date deposition_date	2007-11-09
Structure title title	Crystal structure of the NM23-H2 transcription factor complex with GDP
Keywords keywords	;transcription factor, cancer, kinase, nm23 gen, hexamer, Activator, Anti-oncogene, ATP-binding, Cell cycle, DNA-binding, Magnesium, Metal-binding, Nucleotide metabolism, Nucleotide-binding, Nucleus, Phosphorylation, Transcription regulation, Transferase ;; TRANSFERASE
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.

3bbf__assembly_1__model_1

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

Download this curve (.dat)

3bbf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bbf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.52 Å
Rg (electron density)	27.42 Å
Total Rg	28.23 Å
Atom count	7450
Residues	906
Excluded volume	132710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bbf__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Nucleoside diphosphate kinase B
Molecular weight formula_weight	17192.9 kDa
EC 编号 ec_number	2.7.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	8276

ANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEELVDYKSCAHDWVYE

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	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	658

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3bbfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d3bbfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d3bbfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d3bbfd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d3bbfe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d3bbff_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

CATH v4.4 (6 domains)

Domain ID domain_id	3bbfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	3bbfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	3bbfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	3bbfD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	3bbfE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	3bbfF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

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Unit-cell length a length_a	69.750 Å
Unit-cell length b length_b	86.780 Å
Unit-cell length c length_c	159.120 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1981
R_work r_work	0.1961
R_free r_free	0.2359

Crystal structure of the NM23-H2 transcription factor complex with GDP

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

Nucleoside diphosphate kinase B

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

3bbf__assembly_1__model_1

3bbf__assembly_1__model_1 | I(q)

3bbf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Crystal structure of the NM23-H2 transcription factor complex with GDP

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

Nucleoside diphosphate kinase B

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

3bbf__assembly_1__model_1

3bbf__assembly_1__model_1 | I(q)

3bbf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)