SAXSdb — 1svj

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

Potassium-transporting ATPase B chain

Escherichia coli

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 316–451	Fragment：N-terminal domain	No other associated polymer	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

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 1SVJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U7Q THE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF KDPB Deposited 2004-08-04	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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

26 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATKB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–156； UniProt 316–451

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	1svj
Deposition date deposition_date	2004-03-29
Structure title title	The solution structure of the nucleotide binding domain of KdpB
Keywords keywords	alpha-beta sandwich, HYDROLASE; HYDROLASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.45 Å
Radius of gyration Rg (electron density) rg_electron	13.92 Å
Forward intensity I(0) i0	4680720.00
Molecular weight molecular_weight	14800.0 kDa
Excluded volume excluded_volume	18372 Å³
Envelope volume envelope_volume	20732 Å³
Hydration-shell volume shell_volume	12495 Å³
Envelope diameter envelope_diameter	50.4 Å
Shell Rg shell_rg	19.85 Å
Envelope Rg envelope_rg	14.55 Å
Shape Rg shape_rg	13.91 Å
Total Rg total_rg	15.15 Å
Total atoms total_atoms	2098
Residues n_residues	136
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	52.4 Å
Rg (real space) rg_real	15.36 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	4.6810e+06
I(0) uncertainty (real space) i0_real_error	5.2130e+04
Rg (reciprocal space) rg_reciprocal	15.37 Å
I(0) (reciprocal space) i0_reciprocal	4681000.0000
Solution quality estimate total_estimate	0.8576
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.200
Kurtosis Kurtosis kurtosis	-0.182
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1343000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1svja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamily	d.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family family	d.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

CATH v4.4 (1 domains)

Domain ID domain_id	1svjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

Description description	Potassium-transporting ATPase B chain
Molecular weight formula_weight	17168.3 kDa
EC 编号 ec_number	3.6.3.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2098

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

The solution structure of the nucleotide binding domain of KdpB

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

Potassium-transporting ATPase B chain

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/sv/1svj/1svj.fit
pddf	/app/data/pr_computation/sv/1svj/1svj.pr.out
profile	/app/data/saxs_computation/sv/1svj/1svj.dat