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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P22887 New Search
25PDB entries
25Biological assembly
65chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1B4S STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT Deposited 1998-12-28 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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
2BEF CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3 Deposited 1998-05-26 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.