← Back to search
2a29

The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB

Method: SOLUTION NMR Dmax: 51.5 Å Quality: GOOD
▼

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

Potassium-transporting ATPase B chain

Escherichia coli

UniProt P03960

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：KdpBN, nucleotide binding domain of KdpB 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

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 2A29 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1SVJ The solution structure of the nucleotide binding domain of KdpB Deposited 2004-03-29 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：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 Different construct Different ligand/ion 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 2a29

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2a29
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2a29
Deposition date deposition_date2005-06-22
Structure title titleThe solution structure of the AMP-PNP bound nucleotide binding domain of KdpB
Keywords keywordsALPHA-BETA SANDWICH, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier15.58 Å
Radius of gyration Rg (electron density) rg_electron14.01 Å
Forward intensity I(0) i05297720.00
Molecular weight molecular_weight15306.0 kDa
Excluded volume excluded_volume18766 ų
Envelope volume envelope_volume21255 ų
Hydration-shell volume shell_volume12728 ų
Envelope diameter envelope_diameter53.1 Å
Shell Rg shell_rg20.05 Å
Envelope Rg envelope_rg14.54 Å
Shape Rg shape_rg13.99 Å
Total Rg total_rg15.24 Å
Total atoms total_atoms2142
Residues n_residues136
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax51.5 Å
Rg (real space) rg_real15.48 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real5.2980e+06
I(0) uncertainty (real space) i0_real_error6.5150e+04
Rg (reciprocal space) rg_reciprocal15.49 Å
I(0) (reciprocal space) i0_reciprocal5298000.0000
Solution quality estimate total_estimate0.7922
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.9 Å
Skewness Skewness skewness0.151
Kurtosis Kurtosis kurtosis-0.264
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1214000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2a29a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.220 — Metal cation-transporting ATPase, ATP-binding domain N
Superfamily Superfamily superfamilyd.220.1 — Metal cation-transporting ATPase, ATP-binding domain N
Family Family familyd.220.1.1 — Metal cation-transporting ATPase, ATP-binding domain N

CATH v4.4 (1 domains)

Domain ID domain_id2a29A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily10 — Calcium-transporting ATPase, cytoplasmic domain N
▶

8. Citations (1)

▶

9. Files and Curves (10)