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- PDB-5ldh: STRUCTURE OF THE ACTIVE TERNARY COMPLEX OF PIG HEART LACTATE DEHY... -

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Basic information

Entry
Database: PDB / ID: 5ldh
TitleSTRUCTURE OF THE ACTIVE TERNARY COMPLEX OF PIG HEART LACTATE DEHYDROGENASE WITH S-LAC-NAD AT 2.7 ANGSTROMS RESOLUTION
ComponentsLACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHOH DONOR / NAD ACCEPTR
Function / homology
Function and homology information


Pyruvate metabolism / L-lactate dehydrogenase / carboxylic acid metabolic process / L-lactate dehydrogenase (NAD+) activity / mitochondrial inner membrane
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-LNC / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsGrau, U.M. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 A resolution.
Authors: Grau, U.M. / Trommer, W.E. / Rossmann, M.G.
#1: Journal: Am.Cryst.Assoc.,Abstr.Papers (Summer Meeting) / Year: 1980
Title: The 2.7 Angstroms X-Ray Structure of Pig H4 Ldh/S-Lac-Nad+-A Very Close Representation of the Active Ternary Complex of Lactate Dehydrogenase
Authors: Grau, U.M. / Rossmann, M.G.
#2: Journal: Biochemistry / Year: 1978
Title: Combined Coenzyme-Substrate Analogues of Various Dehydrogenases. Synthesis of (3S)-and (3R)-5-(3-Carboxy-3-Hydroxypropyl)Nicotinamide Adenine Dinucleotide and Their Interaction with (S)-and (R) ...Title: Combined Coenzyme-Substrate Analogues of Various Dehydrogenases. Synthesis of (3S)-and (3R)-5-(3-Carboxy-3-Hydroxypropyl)Nicotinamide Adenine Dinucleotide and Their Interaction with (S)-and (R)-Lactate-Specific Dehydrogenases
Authors: Grau, U. / Kapmeyer, H. / Trommer, W.E.
History
DepositionOct 29, 1980Processing site: BNL
Revision 1.0Mar 4, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 31, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / 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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_PDB_matrix / pdbx_database_remark / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 2.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9366
Polymers73,0202
Non-polymers1,9154
Water00
1
A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules

A: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,87112
Polymers146,0414
Non-polymers3,8318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area24770 Å2
ΔGint-148 kcal/mol
Surface area52470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.600, 133.600, 113.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.271631, 0.158285, -0.806013), (0.15823, -0.092201, 0.466799), (-0.806068, 0.466847, 0.363833)
Vector: -30.48687, -53.28395, 0.18015)

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Components

#1: Protein LACTATE DEHYDROGENASE


Mass: 36510.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00336, L-lactate dehydrogenase
#2: Chemical ChemComp-LNC / (3S)-5-(3-CARBOXY-3-HYDROXYPROPYL) NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-LAC-NAD+


Mass: 765.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33N7O17P2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
Has protein modificationY
Nonpolymer detailsTHE COORDINATES OF THE CITRATE ION BOUND TO THE PROTEIN NEAR THE MOLECULAR P-AXIS ARE ONLY ...THE COORDINATES OF THE CITRATE ION BOUND TO THE PROTEIN NEAR THE MOLECULAR P-AXIS ARE ONLY APPROXIMATE. PRESUMABLY THIS ION IS IMPORTANT FOR THE INTEGRITY OF THE TETRAMER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.28 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
134 mg/mlpig H4 LDH1drop
244 mMS-lac-NAD+1drop
41.10 Msodium citrate1drop
3M/50 sodium phosphate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å

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Processing

RefinementHighest resolution: 2.7 Å /
RfactorNum. reflection
Rwork0.196 -
obs-22588
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 128 0 5248
Refinement
*PLUS
Highest resolution: 2.7 Å / Num. reflection obs: 22588 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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