SAXSdb — 1s5z

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

Nucleoside diphosphate kinase, cytosolic

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 Chain D； UniProt 1–155 Chain E； UniProt 1–155 Chain F； UniProt 1–155	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

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 1S5Z	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 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）	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 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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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
2BEF CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3 Deposited 1998-05-26	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） Chain B 1–155（155 aa） Chain C 1–155（155 aa）	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
3FKB Structure of NDPK H122G and tenofovir-diphosphate Deposited 2008-12-16	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 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 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	1s5z
Deposition date deposition_date	2004-01-22
Structure title title	NDP kinase in complex with adenosine phosphonoacetic acid
Keywords keywords	TRANSFERASE; TRANSFERASE
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	28.53 Å
Radius of gyration Rg (electron density) rg_electron	27.39 Å
Forward intensity I(0) i0	143249000.00
Molecular weight molecular_weight	97847.0 kDa
Excluded volume excluded_volume	123980 Å³
Envelope volume envelope_volume	147240 Å³
Hydration-shell volume shell_volume	42790 Å³
Envelope diameter envelope_diameter	93.8 Å
Shell Rg shell_rg	36.51 Å
Envelope Rg envelope_rg	27.39 Å
Shape Rg shape_rg	27.41 Å
Total Rg total_rg	28.22 Å
Total atoms total_atoms	6911
Residues n_residues	900
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	89.8 Å
Rg (real space) rg_real	28.34 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.4320e+08
I(0) uncertainty (real space) i0_real_error	2.1790e+06
Rg (reciprocal space) rg_reciprocal	28.42 Å
I(0) (reciprocal space) i0_reciprocal	143300000.0000
Solution quality estimate total_estimate	0.8906
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.065
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42270000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nucleoside diphosphate kinase, cytosolic
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	8058

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	ADENOSINE PHOSPHONOACETIC ACID
Molecular weight formula_weight	389.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1147

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1s5za_
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	d1s5zb_
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	d1s5zc_
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	d1s5zd_
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	d1s5ze_
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	d1s5zf_
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	1s5zA00
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	1s5zB00
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	1s5zC00
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	1s5zD00
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	1s5zE00
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	1s5zF00
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	69.380 Å
Unit-cell length b length_b	104.594 Å
Unit-cell length c length_c	69.569 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.28 °
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	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1870
R_free r_free	0.2390

fit	/app/data/saxs_computation/s5/1s5z/1s5z.fit
pddf	/app/data/pr_computation/s5/1s5z/1s5z.pr.out
profile	/app/data/saxs_computation/s5/1s5z/1s5z.dat

NDP kinase in complex with adenosine phosphonoacetic acid

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

Nucleoside diphosphate kinase, cytosolic

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