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- PDB-6cep: Sus scrofa heart L-lactate dehydrogenase ternary complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 6cep
TitleSus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / ternary complex / heart isoform (H-chain)
Function / homology
Function and homology information


Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / mitochondrial inner membrane / mitochondrion
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 / OXAMIC ACID / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHoffer, E.D. / Andrews, B. / Dunham, C.M. / Dyer, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM068036-014 United States
CitationJournal: Medchemcomm / Year: 2018
Title: Small molecule cores demonstrate non-competitive inhibition of lactate dehydrogenase.
Authors: Andrews, B.A. / Dyer, R.B.
History
DepositionFeb 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase B chain
B: L-lactate dehydrogenase B chain
C: L-lactate dehydrogenase B chain
D: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,61512
Polymers146,6054
Non-polymers3,0108
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25660 Å2
ΔGint-140 kcal/mol
Surface area43210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.120, 137.230, 161.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-lactate dehydrogenase B chain / LDH-B / LDH heart subunit / LDH-H


Mass: 36651.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00336, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, sodium acetate, HEPES, sodium oxamate, NADH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→104.53 Å / Num. obs: 91063 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.66 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.085 / Rrim(I) all: 0.178 / Net I/σ(I): 5.1 / Num. measured all: 387434 / Scaling rejects: 926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.034.31.3871880543890.7570.7271.5691.4100
10.95-104.533.50.06122916630.9930.0350.0718.499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å104.53 Å
Translation2 Å104.53 Å

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Processing

Software
NameVersionClassification
xia20.5.179data reduction
DIALS1.4.5data reduction
Aimless0.5.32data scaling
PHASER2.7.16phasing
PHENIX1.13_2998refinement
Coot0.8.9model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LDH
Resolution: 2→104.532 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.41
RfactorNum. reflection% reflection
Rfree0.2568 1998 2.38 %
Rwork0.2161 --
obs0.2171 83853 92.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.45 Å2 / Biso mean: 26.8061 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: final / Resolution: 2→104.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9977 0 200 747 10924
Biso mean--25.9 31.16 -
Num. residues----1301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05020.3115540.28242216227035
2.0502-2.10560.3001990.2644111421066
2.1056-2.16760.29381360.26015569570589
2.1676-2.23750.30441550.251163066461100
2.2375-2.31750.30211530.235662776430100
2.3175-2.41030.26271540.228462856439100
2.4103-2.520.2791520.240262776429100
2.52-2.65290.2791550.24163066461100
2.6529-2.81910.31431540.244263086462100
2.8191-3.03680.23751540.249663426496100
3.0368-3.34240.26671560.223663796535100
3.3424-3.82610.2411560.184563606516100
3.8261-4.82050.21731570.157264506607100
4.8205-104.67480.19491630.18716669683299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20630.346-0.44690.5771-0.75230.97030.01670.1174-0.0355-0.0802-0.0253-0.17640.02930.4434-0.00390.27580.00610.13520.32370.01240.322321.14572.5244-25.4455
20.12690.19150.09540.522-0.02130.3347-0.00160.1778-0.1044-0.01420.0177-0.1760.15690.12820.00760.06520.02540.01050.1738-0.01670.074618.0129-16.059-5.5438
30.1056-0.12850.11380.51070.1380.31470.0658-0.0992-0.06360.52380.01190.12020.0773-0.05690.06480.2822-0.01710.06280.09190.00960.10646.8014-12.178212.9738
40.6303-0.18860.19590.7626-0.37270.98940.0262-0.2691-0.02950.25770.0339-0.05140.20030.10680.00260.3677-0.0217-0.06370.1709-0.01360.06717.8908-10.058521.1744
50.23230.13180.49950.30520.71041.85430.0931-0.2041-0.04210.0969-0.06350.20090.0248-0.3546-0.01420.442-0.01870.22310.25810.05180.4899-20.075-8.426812.423
60.58880.15360.36640.4401-0.00130.81110.05370.0549-0.1312-0.04360.01120.27930.1065-0.0893-0.01710.0971-0.0218-0.00420.13-0.01870.2037-10.0398-22.5442-9.9117
70.83950.2073-0.22090.5260.0880.40430.07850.0776-0.088-0.25430.02250.04960.0210.0373-0.03210.19950.0173-0.04980.2098-0.02890.1061.4753-10.4493-30.3217
80.09650.1324-0.03390.2262-0.17410.41130.10290.17540.0347-0.35040.0207-0.18570.14740.1183-0.01610.25520.07420.03390.2616-0.0650.15616.5287-15.9744-27.1849
90.14750.11910.04780.44650.26330.50790.00390.1974-0.0556-0.2336-0.00490.13750.19310.0376-0.06370.26970.0359-0.20130.2796-0.10090.222-11.219-17.6124-33.4627
100.0407-0.1665-0.29230.70061.20832.07430.0670.20080.042-0.0009-0.03550.2095-0.0538-0.3175-0.02630.30440.026-0.14550.33130.00760.5192-20.6404-2.4626-26.8811
110.3670.0615-0.15710.15580.08940.1667-0.07220.14330.0599-0.0742-0.06490.32340.01340.0039-0.0905-0.0478-0.0033-0.00560.1665-0.06390.3193-16.279212.9154-11.5826
120.0141-0.0197-0.02130.07520.04480.0274-0.0094-0.0161-0.11230.0476-0.04060.260.062-0.08450.0749-0.10780.03370.34950.1658-0.14970.6023-24.086418.61074.3423
130.513-0.041-0.02020.1880.12740.5367-0.0098-0.078-0.04160.1140.01030.1322-0.0001-0.02920.04850.2228-0.00490.21640.0916-0.01840.1724-9.125710.408710.8199
140.4444-0.2559-0.21290.2150.18160.27210.0061-0.06230.06310.14280.10460.0256-0.06460.03960.0680.36010.01310.21640.0941-0.10280.116-2.42648.836819.3872
150.1991-0.04790.07830.8948-0.48081.2127-0.0923-0.12240.0090.41240.0986-0.07230.16130.10480.00420.34280.04920.08170.158-0.08760.1809-0.437620.835219.8662
160.11480.2411-0.08980.5239-0.17630.0961-0.0427-0.0127-0.08350.1285-0.07550.14150.1471-0.0251-0.04610.0907-0.0290.28720.1323-0.05820.2311-11.24257.77883.954
170.3882-0.0616-0.18320.0189-0.03390.56860.0148-0.1210.02990.13890.02120.0647-0.0607-0.05950.00060.4098-0.05830.43760.2047-0.04030.3909-19.20424.822418.2644
180.709-0.4661-0.02750.63140.29881.21420.03-0.04620.07310.0438-0.01910.074-0.143-0.156-0.00630.5819-0.05480.3750.2715-0.11940.4767-21.351317.645222.862
190.4298-0.10890.27110.0262-0.07010.16870.0665-0.23390.06160.1197-0.05-0.0336-0.2010.20920.00240.3157-0.0167-0.10110.2795-0.07130.225516.40578.403313.0261
200.76420.1571-0.31730.33290.00150.6243-0.06450.04730.0982-0.08050.0156-0.0473-0.05580.0286-0.08580.0738-0.0210.03840.136-0.01730.11959.723122.4758-9.2543
210.90780.1075-0.07430.45570.24180.34280.05070.12640.0658-0.27660.01780.0323-0.085-0.02630.04670.22420.0023-0.06430.25480.00240.0859-0.620610.5599-30.333
220.22110.13670.01140.3810.26250.23260.03130.14620.1031-0.339-0.03720.2439-0.1075-0.10540.07920.214-0.0044-0.0640.28110.00480.1239-2.993314.811-26.954
230.1531-0.0547-0.08920.5478-0.33740.7543-0.00810.19230.1204-0.23560.0336-0.0435-0.21150.1172-0.03740.3683-0.05290.10840.30470.04760.067712.683319.4858-34.3412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 127 )A23 - 127
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 276 )A128 - 276
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 331 )A277 - 331
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )B1 - 21
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 151 )B22 - 151
7X-RAY DIFFRACTION7chain 'B' and (resid 152 through 214 )B152 - 214
8X-RAY DIFFRACTION8chain 'B' and (resid 215 through 265 )B215 - 265
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 332 )B266 - 332
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 22 )C1 - 22
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 94 )C23 - 94
12X-RAY DIFFRACTION12chain 'C' and (resid 95 through 151 )C95 - 151
13X-RAY DIFFRACTION13chain 'C' and (resid 152 through 178 )C152 - 178
14X-RAY DIFFRACTION14chain 'C' and (resid 179 through 214 )C179 - 214
15X-RAY DIFFRACTION15chain 'C' and (resid 215 through 245 )C215 - 245
16X-RAY DIFFRACTION16chain 'C' and (resid 246 through 276 )C246 - 276
17X-RAY DIFFRACTION17chain 'C' and (resid 277 through 309 )C277 - 309
18X-RAY DIFFRACTION18chain 'C' and (resid 310 through 331 )C310 - 331
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 22 )D1 - 22
20X-RAY DIFFRACTION20chain 'D' and (resid 23 through 151 )D23 - 151
21X-RAY DIFFRACTION21chain 'D' and (resid 152 through 214 )D152 - 214
22X-RAY DIFFRACTION22chain 'D' and (resid 215 through 276 )D215 - 276
23X-RAY DIFFRACTION23chain 'D' and (resid 277 through 332 )D277 - 332

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