Current Protein Identity:P03960 New Search
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method 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
1SVJ The solution structure of the nucleotide binding domain of KdpB Deposited 2004-03-29 Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric(1) Consistent with protein count
Chain A 316–451(136 aa) Fragment:N-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6;300 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT
NMR sample composition 1.4MM KDPBN U-15N,13C, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE; 1.2MM KDPBN U-15N, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE
Resolution not provided
1U7Q THE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF KDPB Deposited 2004-08-04 Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric(1) Consistent with protein count
Chain A 316–451(136 aa)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6;300 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT
NMR sample composition 1.4MM U-15N,13C KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE; 1.2MM U-15N KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE
Resolution not provided
2A00 The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB Deposited 2005-06-15 Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric(1) Consistent with protein count
Chain A 316–451(136 aa) Fragment:KdpBN, nucleotide binding domain of KdpB
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SOLUTION NMR
NMR measurement conditions pH 6;300 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT
NMR sample composition 1.0MM U-15N,13C KDPBN, 50MM phosphate buffer, 100MM NACL, 0.05% sodium azide, 15MM ATP- PNP; 1.0MM U-15N KDPBN, 50MM phosphate buffer, 100MM NACL, 0.05% sodium azide, 15MM AMP- PNP
Resolution not provided
2A29 The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB Deposited 2005-06-22 Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric(1) Consistent with protein count
Chain A 316–451(136 aa) Fragment:KdpBN, nucleotide binding domain of KdpB
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SOLUTION NMR
NMR measurement conditions pH 6;300 K;Ionic strength (raw mmCIF value) 100mM NACL;Pressure AMBIENT
NMR sample composition 1.0MM U-15N, 13C KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE, 15MM ATP- PNP; 1.0MM U-15N KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE, 15MM AMP- PNP
Resolution not provided
5MRW Structure of the KdpFABC complex Deposited 2016-12-27 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 9–682(674 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 1 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;291 K;20% (w/v) PEG3350, 0.5-1.0 M NaCl, 0.05 mM sodium citrate pH 5.5.
Resolution 2.90 Å R-free 0.275
5MRW Structure of the KdpFABC complex Deposited 2016-12-27 Assembly 2 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain F 9–682(674 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 1 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;291 K;20% (w/v) PEG3350, 0.5-1.0 M NaCl, 0.05 mM sodium citrate pH 5.5.
Resolution 2.90 Å R-free 0.275
5MRW Structure of the KdpFABC complex Deposited 2016-12-27 Assembly 3 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain J 9–682(674 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 1 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 BOG octyl beta-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP;pH 5.5;291 K;20% (w/v) PEG3350, 0.5-1.0 M NaCl, 0.05 mM sodium citrate pH 5.5.
Resolution 2.90 Å R-free 0.275
6HRA Cryo-EM structure of the KdpFABC complex in an E1 outward-facing state (state 1) Deposited 2018-09-26 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.012% DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6HRB Cryo-EM structure of the KdpFABC complex in an E2 inward-facing state (state 2) Deposited 2018-09-26 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.012% DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7BGY Cryo-EM Structure of KdpFABC in E2Pi state with MgF4 Deposited 2021-01-09 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Mutation:S162A PEV (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MG MAGNESIUM ION × 1 MF4 TETRAFLUOROMAGNESATE(2-) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5;A 10x stock solution of MgF4 was added to the protein mixture containing all other buffer components to produce final concentrations 1 mM MgCl2 and 10 mM NaF.
cryo-EM vitrification conditions Cryogen ETHANE;3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
Resolution 2.90 Å
7BH1 Cryo-EM Structure of KdpFABC in E1 state with K Deposited 2021-01-09 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Mutation:S162A K POTASSIUM ION × 1 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE;3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
Resolution 3.38 Å
7BH2 Cryo-EM Structure of KdpFABC in E2Pi state with BeF3 and K+ Deposited 2021-01-09 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Mutation:S162A K POTASSIUM ION × 2 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5;The beryllium fluoride in the buffer was added to the protein mixture containing all other buffer components in the form of a pre-incubated mixture, at a 1:10 volume, to produce the final concentrations 2.5 mM BeSO4 and 10 mM NaF.
cryo-EM vitrification conditions Cryogen ETHANE;3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
Resolution 3.00 Å
7LC3 CryoEM Structure of KdpFABC in E1-ATP state Deposited 2021-01-09 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Mutation:S162A K POTASSIUM ION × 2 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MG MAGNESIUM ION × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5;AMPPCP was added to the protein after size-exclusion chromatography and incubated 1 hr prior to freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7LC6 Cryo-EM Structure of KdpFABC in E2-P state with BeF3 Deposited 2021-01-09 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Mutation:S162A K POTASSIUM ION × 1 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5;The beryllium fluoride in the buffer was added to the protein mixture containing all other buffer components in the form of a pre-incubated mixture with the final concentrations 2.5 mM BeSO4 and 10 mM NaF.
cryo-EM vitrification conditions Cryogen ETHANE;3 uL of protein mixture applied to grid. Blot time 4 seconds, blot force 0, no wait before plunging.
Resolution 3.70 Å
7ZRD Cryo-EM map of the WT KdpFABC complex in the E1-P tight conformation, stabilised with the inhibitor orthovanadate Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 9 CDL CARDIOLIPIN × 2 VO4 VANADATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7ZRE Cryo-EM map of the WT KdpFABC complex in the E1-P tight conformation, under turnover conditions Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 9 CDL CARDIOLIPIN × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7ZRG Cryo-EM map of the WT KdpFABC complex in the E1_ATPearly conformation, under turnover conditions Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 7 CDL CARDIOLIPIN × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7ZRH Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+ Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 7 CDL CARDIOLIPIN × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
7ZRI Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+ Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 7 CDL CARDIOLIPIN × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7ZRJ Cryo-EM structure of the KdpFABC complex in a nucleotide-free E1 conformation loaded with K+ Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 7 CDL CARDIOLIPIN × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
7ZRK Cryo-EM map of the WT KdpFABC complex in the E1-P_ADP conformation, under turnover conditions Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 12 CDL CARDIOLIPIN × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
7ZRL Cryo-EM map of the unphosphorylated KdpFABC complex in the E2-P conformation, under turnover conditions Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.00 Å
7ZRM Cryo-EM map of the unphosphorylated KdpFABC complex in the E1-P_ADP conformation, under turnover conditions Deposited 2022-05-04 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8;10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
9OC4 High-resolution cryo-EM structure of KdpFABC in the E1P-ADP state in lipid nanodisc Deposited 2025-04-23 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 2 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
9ZWK High-resolution cryo-EM structure of KdpFABC in the E1 state in lipid nanodisc Deposited 2026-01-03 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Not recorded K POTASSIUM ION × 3 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
9ZWL High-resolution cryo-EM structure of KdpFABC in the E1-ATP state in lipid nanodisc Deposited 2026-01-03 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Not recorded K POTASSIUM ION × 3 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP, 2mM MgCl2, 1mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
9ZWM High-resolution cryo-EM structure of KdpFABC in the E1P state in lipid nanodisc Deposited 2026-01-03 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.25 Å
9ZWN High-resolution cryo-EM structure of KdpFABC in the E2P state in lipid nanodisc Deposited 2026-01-03 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Non-standard monomer:Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
9ZWO High-resolution cryo-EM structure of KdpFABC in the E2 state in lipid nanodisc Deposited 2026-01-03 Assembly 1 Protein heterocomplex Heteromer;Protein × 4 PDB declaration: tetrameric(4) Consistent with protein count
Chain B 1–682(682 aa)
Not recorded K POTASSIUM ION × 2 9Y0 (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4;20 mM Tris pH 7.4, 100 mM KCl, and 0.5 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å