[English] 日本語
Yorodumi
- PDB-5nqq: Rabbit Muscle L-lactate dehydrogenase in complex with NADH and ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nqq
TitleRabbit Muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / oxaloacetate
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXALOACETATE ION / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.872 Å
AuthorsLuisi, B.F. / Olin-Sandoval, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization.
Authors: Alam, M.T. / Olin-Sandoval, V. / Stincone, A. / Keller, M.A. / Zelezniak, A. / Luisi, B.F. / Ralser, M.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,70214
Polymers146,3944
Non-polymers3,30810
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27900 Å2
ΔGint-244 kcal/mol
Surface area42490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.373, 138.763, 74.567
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / LDH muscle subunit / LDH-M


Mass: 36598.547 Da / Num. of mol.: 4 / Mutation: THR 248 TO SER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LDHA / Production host: Escherichia coli (E. coli) / References: UniProt: P13491, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% wt/v PEG 3350, 50 mM Bis-tris propane pH 6.5 and 100 mM NaF

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.872→29.42 Å / Num. obs: 220343 / % possible obs: 98.9 % / Redundancy: 6.6 % / Net I/σ(I): 14

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H3F

3h3f


Resolution: 1.872→29.416 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.07
RfactorNum. reflection% reflectionSelection details
Rfree0.199 11040 5.01 %Random selection
Rwork0.17 ---
obs0.1715 112037 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.872→29.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10163 0 214 751 11128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210610
X-RAY DIFFRACTIONf_angle_d1.22714396
X-RAY DIFFRACTIONf_dihedral_angle_d18.2296328
X-RAY DIFFRACTIONf_chiral_restr0.0671688
X-RAY DIFFRACTIONf_plane_restr0.0071775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8724-1.89360.37712860.38154722X-RAY DIFFRACTION67
1.8936-1.91590.34413510.31237116X-RAY DIFFRACTION99
1.9159-1.93930.34913290.30557001X-RAY DIFFRACTION99
1.9393-1.96380.32233660.29117083X-RAY DIFFRACTION99
1.9638-1.98970.27843830.26426881X-RAY DIFFRACTION98
1.9897-2.01690.25163330.26657084X-RAY DIFFRACTION99
2.0169-2.04570.29263650.25626985X-RAY DIFFRACTION99
2.0457-2.07620.26023860.24537035X-RAY DIFFRACTION99
2.0762-2.10870.27143060.22817081X-RAY DIFFRACTION99
2.1087-2.14320.24453770.20886973X-RAY DIFFRACTION99
2.1432-2.18020.223860.20177054X-RAY DIFFRACTION99
2.1802-2.21980.23523730.1937088X-RAY DIFFRACTION100
2.2198-2.26250.2323390.17437153X-RAY DIFFRACTION100
2.2625-2.30870.22254470.16556989X-RAY DIFFRACTION100
2.3087-2.35880.19384430.15797077X-RAY DIFFRACTION100
2.3588-2.41370.21083850.15557107X-RAY DIFFRACTION100
2.4137-2.4740.19393400.16157100X-RAY DIFFRACTION100
2.474-2.54090.19493890.15247058X-RAY DIFFRACTION100
2.5409-2.61560.17853140.15387180X-RAY DIFFRACTION100
2.6156-2.70.20373550.15427070X-RAY DIFFRACTION100
2.7-2.79640.19034460.15327110X-RAY DIFFRACTION100
2.7964-2.90830.20653450.16057089X-RAY DIFFRACTION100
2.9083-3.04050.20724340.16026956X-RAY DIFFRACTION100
3.0405-3.20060.17373780.16237099X-RAY DIFFRACTION100
3.2006-3.40090.19823350.15697174X-RAY DIFFRACTION100
3.4009-3.6630.18423930.15676988X-RAY DIFFRACTION99
3.663-4.03080.18063560.14417053X-RAY DIFFRACTION99
4.0308-4.61210.15443740.13096955X-RAY DIFFRACTION98
4.6121-5.80340.14793360.13797063X-RAY DIFFRACTION99
5.8034-29.41920.16743900.15956979X-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://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