[English] 日本語
Yorodumi
- PDB-5zjd: Lactate dehydrogenase with NADH and MLA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zjd
TitleLactate dehydrogenase with NADH and MLA
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / LDHA / NADH
Function / homology
Function and homology information


oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol
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
MALONATE ION / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsHan, C.W. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015R1D1A1A01059594 Korea, Republic Of
CitationJournal: Cancers (Basel) / Year: 2019
Title: Machilin A Inhibits Tumor Growth and Macrophage M2 Polarization Through the Reduction of Lactic Acid.
Authors: Chung, T.-W. / Kim, E.-Y. / Han, C.W. / Park, S.Y. / Jeong, M.S. / Yoon, D. / Choi, H.-J. / Jin, L. / Park, M.-J. / Kwon, Y.J. / Lee, H. / Kim, K.-J. / Park, K.H. / Kim, S. / Jang, S.B. / Ha, K.-T.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,59924
Polymers299,4598
Non-polymers6,14016
Water7,476415
1
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,79912
Polymers149,7294
Non-polymers3,0708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27340 Å2
ΔGint-140 kcal/mol
Surface area41560 Å2
MethodPISA
2
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,79912
Polymers149,7294
Non-polymers3,0708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27330 Å2
ΔGint-140 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.007, 265.691, 88.006
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59


Mass: 37432.355 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 8% Tacsimate (pH 7.0), 20% polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.394→29.803 Å / Num. obs: 103853 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.3
Reflection shellResolution: 2.394→2.4208 Å / Rmerge(I) obs: 0.309 / Num. unique obs: 1212123

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OKN

4okn


Resolution: 2.394→29.803 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.67
RfactorNum. reflection% reflection
Rfree0.2581 5073 4.88 %
Rwork0.1869 --
obs0.1904 103852 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.394→29.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20544 0 408 415 21367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821331
X-RAY DIFFRACTIONf_angle_d1.0528912
X-RAY DIFFRACTIONf_dihedral_angle_d9.33712776
X-RAY DIFFRACTIONf_chiral_restr0.0533376
X-RAY DIFFRACTIONf_plane_restr0.0053592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3936-2.42080.31461390.25082488X-RAY DIFFRACTION69
2.4208-2.44930.31751540.24882975X-RAY DIFFRACTION84
2.4493-2.47920.31541740.24892977X-RAY DIFFRACTION83
2.4792-2.51050.31581500.24363020X-RAY DIFFRACTION83
2.5105-2.54350.2861630.24353087X-RAY DIFFRACTION87
2.5435-2.57840.36881590.24543119X-RAY DIFFRACTION86
2.5784-2.61520.34321930.25173097X-RAY DIFFRACTION86
2.6152-2.65420.30091460.23613168X-RAY DIFFRACTION89
2.6542-2.69560.29571680.23083194X-RAY DIFFRACTION88
2.6956-2.73980.3061530.233150X-RAY DIFFRACTION87
2.7398-2.7870.32781620.22823197X-RAY DIFFRACTION89
2.787-2.83770.34451520.23113195X-RAY DIFFRACTION87
2.8377-2.89220.31591720.22653158X-RAY DIFFRACTION89
2.8922-2.95120.34581570.21823197X-RAY DIFFRACTION88
2.9512-3.01530.29961550.21313156X-RAY DIFFRACTION89
3.0153-3.08540.28171600.21683250X-RAY DIFFRACTION89
3.0854-3.16240.34391460.21083242X-RAY DIFFRACTION90
3.1624-3.24780.25261780.20443353X-RAY DIFFRACTION92
3.2478-3.34330.27331670.20593343X-RAY DIFFRACTION94
3.3433-3.4510.2751550.20743546X-RAY DIFFRACTION97
3.451-3.57420.26671930.19623518X-RAY DIFFRACTION98
3.5742-3.7170.23651980.18213533X-RAY DIFFRACTION99
3.717-3.88590.26771950.1733598X-RAY DIFFRACTION100
3.8859-4.09030.24141910.1653579X-RAY DIFFRACTION100
4.0903-4.34580.20381880.14643634X-RAY DIFFRACTION100
4.3458-4.68020.18991700.13893599X-RAY DIFFRACTION99
4.6802-5.1490.22221700.14123593X-RAY DIFFRACTION100
5.149-5.8890.22182020.17073597X-RAY DIFFRACTION99
5.889-7.40070.22691880.16373601X-RAY DIFFRACTION100
7.4007-29.80570.17181750.13823615X-RAY DIFFRACTION99

+
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://pdbjlvh1.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