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- PDB-1aqf: PYRUVATE KINASE FROM RABBIT MUSCLE WITH MG, K, AND L-PHOSPHOLACTATE -

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Basic information

Entry
Database: PDB / ID: 1aqf
TitlePYRUVATE KINASE FROM RABBIT MUSCLE WITH MG, K, AND L-PHOSPHOLACTATE
ComponentsPYRUVATE KINASE
KeywordsTRANSFERASE / PYRUVATE KINASE / RABBIT MUSCLE / DOMAIN MOVEMENT / POTASSIUM BINDING
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / non-specific serine/threonine protein kinase ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / non-specific serine/threonine protein kinase / mRNA binding / magnesium ion binding / ATP binding / nucleus
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / L-PHOSPHOLACTATE / Pyruvate kinase PKM
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsLarsen, T.M. / Benning, M.M. / Wesenberg, G.E. / Rayment, I. / Reed, G.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 1997
Title: Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution.
Authors: Larsen, T.M. / Benning, M.M. / Wesenberg, G.E. / Rayment, I. / Reed, G.H.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,85832
Polymers463,9918
Non-polymers1,86824
Water3,495194
1
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,92916
Polymers231,9954
Non-polymers93412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-144 kcal/mol
Surface area73430 Å2
MethodPISA
2
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,92916
Polymers231,9954
Non-polymers93412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-145 kcal/mol
Surface area69590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.400, 112.600, 171.200
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PYRUVATE KINASE


Mass: 57998.820 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P11974, pyruvate kinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEQ / L-PHOSPHOLACTATE


Mass: 170.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.3 mg/mlenzyme11
27.7 %PEG800011
30.21 M11KCl
45 mM11MgCl2
55 mMATP11
64.5 mML-lactate11
750 mMHEPES11
80.12 mMAp5A11

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Data collection

DiffractionMean temperature: 276 K
DetectorDate: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 76181 / % possible obs: 94 % / Observed criterion σ(I): 3 / Num. measured all: 736673 / Rmerge(I) obs: 0.075

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Processing

SoftwareName: TNT / Version: 5E / Classification: refinement
RefinementResolution: 2.7→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.196 --
obs-141340 93 %
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31209 0 96 194 31499
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_dihedral_angle_d20.553
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0070.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.015
Software
*PLUS
Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.553
X-RAY DIFFRACTIONt_plane_restr0.0070.012

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