1b99

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Method: X-RAY DIFFRACTION

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

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)

Dictyostelium discoideum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE × 1 PYROPHOSPHATE 2- × 5 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDKC_DICDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 1–155 Author chain B； PDBConstruct 1–155； UniProt 1–155 Author chain C； PDBConstruct 1–155； UniProt 1–155 Author chain D； PDBConstruct 1–155； UniProt 1–155 Author chain E； PDBConstruct 1–155； UniProt 1–155 Author chain F； PDBConstruct 1–155； UniProt 1–155

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	1b99
Deposition date deposition_date	1999-02-22
Structure title title	3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
Keywords keywords	PHOSPHOTRANSFERASE, ANTIVIRAL AGENT, FLUOROURIDINE, 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.

1b99__assembly_1__model_1

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

Download this curve (.dat)

1b99__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1b99__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.66 Å
Rg (electron density)	27.52 Å
Total Rg	28.34 Å
Atom count	6951
Residues	900
Excluded volume	124360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1b99__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 (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
Molecular weight formula_weight	16816.3 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	6970

MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

Source Source

Source organism organism	Dictyostelium discoideum
NCBI taxonomy ID ncbi_taxonomy_id	44689
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	390.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1b99a_
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	d1b99b_
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	d1b99c_
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	d1b99d_
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	d1b99e_
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	d1b99f_
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	1b99A00
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	1b99B00
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	1b99C00
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	1b99D00
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	1b99E00
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	1b99F00
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	70.020 Å
Unit-cell length b length_b	105.310 Å
Unit-cell length c length_c	70.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.2070
R_free r_free	0.3040

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

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

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)

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

1b99__assembly_1__model_1

1b99__assembly_1__model_1 | I(q)

1b99__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

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

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)

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

1b99__assembly_1__model_1

1b99__assembly_1__model_1 | I(q)

1b99__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (3)