[English] 日本語
Yorodumi
- PDB-3ldh: A comparison of the structures of apo dogfish m4 lactate dehydrog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ldh
TitleA comparison of the structures of apo dogfish m4 lactate dehydrogenase and its ternary complexes
ComponentsLACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHOH DONOR / NAD ACCEPTOR
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / cytoplasm
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRUVIC ACID / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesSqualus acanthias (spiny dogfish)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWhite, J.L. / Hackert, M.L. / Buehner, M. / Adams, M.J. / Ford, G.C. / Lentzjunior, P.J. / Smiley, I.E. / Steindel, S.J. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1976
Title: A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes.
Authors: White, J.L. / Hackert, M.L. / Buehner, M. / Adams, M.J. / Ford, G.C. / Lentz Jr., P.J. / Smiley, I.E. / Steindel, S.J. / Rossmann, M.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Structural Adaptations of Lactate Dehydrogenase Isozymes
Authors: Eventoff, W. / Rossmann, M.G. / Taylor, S.S. / Torff, H.-J. / Meyer, H. / Keil, W. / Kiltz, H.-H.
#2: Journal: J.Mol.Biol. / Year: 1975
Title: A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex
Authors: White, J. / Rossmann, M.G. / Ford, G.C.
#3: Journal: Isozymes-Molecular Structure / Year: 1975
Title: A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase
Authors: Eventoff, W. / Hackert, M.L. / Steindel, S.J. / Rossmann, M.G.
#4: Journal: The Enzymes,Third Edition / Year: 1975
Title: Lactate Dehydrogenase
Authors: Holbrook, J.J. / Liljas, A. / Steindel, S.J. / Rossmann, M.G.
#5: Journal: Annu.Rev.Biochem. / Year: 1974
Title: X-Ray Studies of Protein Interactions
Authors: Liljas, A. / Rossmann, M.G.
#6: Journal: Nature / Year: 1974
Title: Chemical and Biological Evolution of a Nucleotide Binding Protein
Authors: Rossmann, M.G. / Moras, D. / Olsen, K.W.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: Recognition of Structural Domains in Globular Proteins
Authors: Rossmann, M.G. / Liljas, A.
#8: Journal: Biochem.Biophys.Res.Commun. / Year: 1973
Title: Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase
Authors: Adams, M.J. / Ford, G.C. / Liljas, A. / Rossmann, M.G.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Structure-Function Relationships in Lactate Dehydrogenase
Authors: Adams, M.J. / Buehner, M. / Chandrasekhar, K. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rossmann, M.G. / Smiley, I.E. / Allison, W.S. / Everse, J. / Kaplan, N.O. / Taylor, S.S.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase
Authors: Taylor, S.S. / Oxley, S.S. / Allison, W.S. / Kaplan, N.O.
#11: Journal: J.Mol.Biol. / Year: 1973
Title: Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases
Authors: Rossmann, M.G. / Adams, M.J. / Buehner, M. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rao, S.T. / Banaszak, L.J. / Hill, E. / Tsernoglou, D. / Webb, L.
#12: Journal: J.Mol.Biol. / Year: 1973
Title: Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase
Authors: Adams, M.J. / Liljas, A. / Rossmann, M.G.
#13: Journal: J.Mol.Biol. / Year: 1973
Title: Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase
Authors: Mcphersonjunior, A.
#14: Journal: J.Mol.Biol. / Year: 1973
Title: Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase
Authors: Chandrasekhar, K. / Mcphersonjunior, A. / Adams, M.J. / Rossmann, M.G.
#15: Journal: J.Mol.Biol. / Year: 1971
Title: The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme
Authors: Smiley, I.E. / Koekoek, R. / Adams, M.J. / Rossmann, M.G.
#16: Journal: Nature / Year: 1970
Title: Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution
Authors: Adams, M.J. / Ford, G.C. / Koekoek, R. / Lentzjunior, P.J. / Mcphersonjunior, A. / Rossmann, M.G. / Smiley, I.E. / Schevitz, R.W. / Wonacott, A.J.
#17: Journal: J.Mol.Biol. / Year: 1969
Title: Low Resolution Study of Crystalline L-Lactate Dehydrogenase
Authors: Adams, M.J. / Haas, D.J. / Jeffery, B.A. / Mcphersonjunior, A. / Mermall, H.L. / Rossmann, M.G. / Schevitz, R.W. / Wonacott, A.J.
#18: Journal: Proc.Natl.Acad.Sci.USA / Year: 1967
Title: The Crystal Structure of Lactic Dehydrogenase
Authors: Rossmann, M.G. / Jeffery, B.A. / Main, P. / Warren, S.
#19: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#20: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionJun 6, 1974Processing site: BNL
Revision 1.0Apr 29, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2013Group: Derived calculations
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2303
Polymers36,4781
Non-polymers7512
Water00
1
A: LACTATE DEHYDROGENASE
hetero molecules

A: LACTATE DEHYDROGENASE
hetero molecules

A: LACTATE DEHYDROGENASE
hetero molecules

A: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,91912
Polymers145,9134
Non-polymers3,0068
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: LACTATE DEHYDROGENASE
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 37.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)37,2303
Polymers36,4781
Non-polymers7512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)134.500, 134.500, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MC4212
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(1), (-1), (-1)
2generate(-1), (1), (-1)
3generate(-1), (-1), (1)
DetailsNON-CRYSTALLOGRAPHIC SYMMETRY ELEMENTS CORRESPONDING TO THE THREE ORTHOGONAL MOLECULAR SYMMETRY AXES ARE EXPRESSED IN THE MTRIX RECORDS BELOW.

-
Components

#1: Protein LACTATE DEHYDROGENASE


Mass: 36478.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Squalus acanthias (spiny dogfish) / References: UniProt: P00341, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-9 mg/mlenzyme11
21.8 Mammonium sulfate12
40.0039 Mprotein12
50.1 Mpyruvate12
3Tris-HCl12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementHighest resolution: 3 Å
Details: SPACE GROUP C 4 21 2 (WHICH, MORE PROPERLY, SHOULD BE NAMED C 4 2 21) IS A NON-STANDARD REPRESENTATION OF SPACE GROUP P 4 21 2. IN THIS CASE THE AXES OF THE UNIT CELL ARE CONSIDERED TO BE LEFT-HANDED.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 50 0 2604
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more