SAXSdb — 2bef

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

NUCLEOSIDE DIPHOSPHATE KINASE

Dictyostelium discoideum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–155 Chain B； UniProt 1–155 Chain C； UniProt 1–155	Not recorded	MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；HANGING DROP, SEEDING, 32% PEG550, 50MM TRIS PH 7.5, 20MM MGCL2, 25MM NAF, 1MM BECL2	Resolution 2.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2BEF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4S STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT Deposited 1998-12-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Mutation：H122G Mutation：H122G Mutation：H122G	PO4 PHOSPHATE ION × 6 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.305
1B99 3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1999-02-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Fragment：HEXAMER Chain B 1–155（155 aa） Fragment：HEXAMER Chain C 1–155（155 aa） Fragment：HEXAMER Chain D 1–155（155 aa） Fragment：HEXAMER Chain E 1–155（155 aa） Fragment：HEXAMER Chain F 1–155（155 aa） Fragment：HEXAMER	Not recorded	FUP 2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.304
1BUX 3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1998-09-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Not recorded	PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.312
1F3F STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX Deposited 2000-06-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Mutation：H122G Mutation：H122G Mutation：H122G	MG MAGNESIUM ION × 6 D4T 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE × 6 PO4 PHOSPHATE ION × 2 D4D 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.85 Å R-free 0.234
1F6T STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX Deposited 2000-06-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 6 TBD 2-DEOXY-THYMIDINE-5-ALPHA BORANO DIPHOSPHATE (ISOMER RP) × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.92 Å R-free 0.274
1HHQ Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase Deposited 2000-12-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa）	Mutation：YES	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH7.5, 1 M AS, 20MM MGCL2 IN WELL: 2M AS, 50MM TRISHCL PH7.5, 20MM MGCL2, pH 7.50	Resolution 2.10 Å R-free 0.255
1HIY Binding of nucleotides to NDP kinase Deposited 2001-01-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Not recorded	3AN 3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH8.5, 8.5MM 3'-AMINO-ADP,15-16% PEG550, 20MM MGCL2 IN WELL: 30-32% PEG550, 50MM TRISHCL PH8.5., pH 8.50	Resolution 2.60 Å R-free 0.325
1HLW STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE Deposited 2000-12-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa）	Mutation：H122A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；PEG 600, Magnesium Chloride, Tris Hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.208
1KDN STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1996-09-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 6 AF3 ALUMINUM FLUORIDE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.179
1LEO P100S NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1996-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 6–155（150 aa）	Mutation：P100S	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1LWX AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1997-04-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Mutation：N119A Mutation：N119A Mutation：N119A	MG MAGNESIUM ION × 4 AZD 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.280
1MN7 NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP Deposited 2002-09-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa）	Mutation：H122G N119S F64W Mutation：H122G N119S F64W	MG MAGNESIUM ION × 6 ABT 3'-AZIDO-3'-DEOXY-THYMIDINE-5'-ALPHA BORANO TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG550, mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.15 Å R-free 0.295
1MN9 NDP kinase mutant (H122G) complex with RTP Deposited 2002-09-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	Mutation：H122G Mutation：H122G Mutation：H122G	MG MAGNESIUM ION × 6 RTP RIBAVIRIN TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 550, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.249
1NCL THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES Deposited 1996-03-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 6–155（150 aa）	Mutation：P105G	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1NDC X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION Deposited 1994-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 6 TYD THYMIDINE-5'-DIPHOSPHATE × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1NDK X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1993-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1NDP ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE Deposited 1993-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1NPK REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE DIPHOSPHATE KINASE AT 1,8 ANGSTROMS RESOLUTION Deposited 1994-07-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–155（154 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1NSP MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM Deposited 1995-04-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1PAE nucleoside diphosphate kinase Deposited 2003-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain X 1–155（155 aa）	Mutation：H122C Non-standard monomer：Yes (specific site not provided by mmCIF)	SE SELENIUM ATOM × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 6000, magnesium chloride,Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.232
1S5Z NDP kinase in complex with adenosine phosphonoacetic acid Deposited 2004-01-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa） Chain D 1–155（155 aa） Chain E 1–155（155 aa） Chain F 1–155（155 aa）	Not recorded	SON ADENOSINE PHOSPHONOACETIC ACID × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.239
3FKB Structure of NDPK H122G and tenofovir-diphosphate Deposited 2008-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa） Chain D 1–155（155 aa） Chain E 1–155（155 aa） Chain F 1–155（155 aa）	Mutation：H122G Mutation：H122G Mutation：H122G Mutation：H122G Mutation：H122G Mutation：H122G	TNM [(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid × 5 MG MAGNESIUM ION × 6 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 2 TNV [2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25% PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.205
4C6A High Resolution Structure of the Nucleoside diphosphate kinase Deposited 2013-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–155（154 aa）	Mutation：YES	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；26% PEG 1000, 100MM TRIS PH7.5	Resolution 1.25 Å R-free 0.172
4CP5 ndpK in complex with (Rp)-SPMPApp Deposited 2014-01-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–155（155 aa） Chain B 1–155（155 aa） Chain C 1–155（155 aa） Chain D 1–155（155 aa） Chain E 1–155（155 aa） Chain F 1–155（155 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	EOI [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate × 6	X-RAY DIFFRACTION X-ray crystallization conditions 26% PEG 1000 100MM TRIS PH7.5	Resolution 2.32 Å R-free 0.246

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

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

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	2bef
Deposition date deposition_date	1998-05-26
Structure title title	CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3
Keywords keywords	PHOSPHOTRANSFERASE, NUCLEOSIDE DIPHOSPHATE KINASE, PHOSPHORYL TRANSFER, BERYLLIUM FLUORIDE; PHOSPHOTRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.18 Å
Radius of gyration Rg (electron density) rg_electron	24.50 Å
Forward intensity I(0) i0	41362200.00
Molecular weight molecular_weight	50251.0 kDa
Excluded volume excluded_volume	63101 Å³
Envelope volume envelope_volume	74529 Å³
Hydration-shell volume shell_volume	25279 Å³
Envelope diameter envelope_diameter	79.7 Å
Shell Rg shell_rg	31.69 Å
Envelope Rg envelope_rg	24.72 Å
Shape Rg shape_rg	24.51 Å
Total Rg total_rg	25.27 Å
Total atoms total_atoms	3537
Residues n_residues	450
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	78.7 Å
Rg (real space) rg_real	25.12 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.1360e+07
I(0) uncertainty (real space) i0_real_error	5.6490e+05
Rg (reciprocal space) rg_reciprocal	25.14 Å
I(0) (reciprocal space) i0_reciprocal	41360000.0000
Solution quality estimate total_estimate	0.9088
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.183
Kurtosis Kurtosis kurtosis	-0.682
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18450000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3757

MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

来源 Source

来源生物 organism	Dictyostelium discoideum
NCBI Class编号 ncbi_taxonomy_id	44689
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2befa_
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	d2befb_
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	d2befc_
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 (3 domains)

Domain ID domain_id	2befA00
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	2befB00
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	2befC00
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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8. Citations (1)

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Unit-cell length a length_a	71.560 Å
Unit-cell length b length_b	71.560 Å
Unit-cell length c length_c	153.750 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	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	—

fit	/app/data/saxs_computation/be/2bef/2bef.fit
pddf	/app/data/pr_computation/be/2bef/2bef.pr.out
profile	/app/data/saxs_computation/be/2bef/2bef.dat

CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3

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

NUCLEOSIDE DIPHOSPHATE KINASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction