[English] 日本語
Yorodumi
- PDB-2mji: HIFABP_Ketorolac_complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mji
TitleHIFABP_Ketorolac_complex
ComponentsFatty acid-binding protein, intestinal
KeywordsLIPID BINDING PROTEIN / TRANSPORT PROTEIN / Protein-ligand complex / Intestinal Fatty Acid Binding Protein / Human FABP2
Function / homology
Function and homology information


intestinal lipid absorption / apical cortex / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / microvillus / fatty acid transport / fatty acid metabolic process / fatty acid binding / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-KTR / Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsPatil, R. / Laguerre, A. / Wielens, J. / Headey, S. / Williams, M. / Mohanty, B. / Porter, C. / Scanlon, M.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Characterization of two distinct modes of drug binding to human intestinal Fatty Acid binding protein.
Authors: Patil, R. / Laguerre, A. / Wielens, J. / Headey, S.J. / Williams, M.L. / Hughes, M.L. / Mohanty, B. / Porter, C.J. / Scanlon, M.J.
History
DepositionJan 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3532
Polymers15,0981
Non-polymers2551
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Fatty acid-binding protein, intestinal / Fatty acid-binding protein 2 / Intestinal-type fatty acid-binding protein / I-FABP


Mass: 15098.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP2, FABPI / Production host: Escherichia coli (E. coli) / References: UniProt: P12104
#2: Chemical ChemComp-KTR / (1R)-5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid / Ketorolac / Ketorolac


Mass: 255.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO3 / Comment: antiinflammatory*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HN(CA)CB
1423D CBCA(CO)NH
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D 1H-15N NOESY
1823D HNCA
1923D HNCO
11023D HN(CA)CB
11113D 1H-13C NOESY aliphatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] HIFABP, 10 mM 5-benzoyl,3-dihydro-1H-pyrrolizine-1-carboxylic acid, 50 mM NaCl, 20 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] HIFABP, 5 mM 5-benzoyl,3-dihydro-1H-pyrrolizine-1-carboxylic acid, 50 mM NaCl, 20 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
30.25 mM [U-13C; U-15N] HIFABP, 2.5 mM 5-benzoyl,3-dihydro-1H-pyrrolizine-1-carboxylic acid, 50 mM NaCl, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHIFABP-1[U-13C; U-15N]1
10 mM5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid-21
50 mMNaCl-31
20 mMMES-41
0.5 mMHIFABP-5[U-13C; U-15N]2
5 mM5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid-62
50 mMNaCl-72
20 mMMES-82
0.25 mMHIFABP-9[U-13C; U-15N]3
2.5 mM5-benzoyl-2,3-dihydro-1H-pyrrolizine-1-carboxylic acid-103
50 mMNaCl-113
20 mMMES-123
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
TOPSPIN3.2Bruker Biospincollection
TOPSPIN3.2Bruker Biospinprocessing
TOPSPIN3.2Bruker Biospindata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKY3.113Goddardpeak picking
SPARKY3.113Goddardchemical shift assignment
VNMRJVariancollection
CNS3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARA4Keller and Wuthrichdata analysis
CARA4Keller and Wuthrichchemical shift assignment
CARA4Keller and Wuthrichpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: TORSIONAL ANGLE DYNAMICS
NMR constraintsNOE constraints total: 1591 / NOE intraresidue total count: 428 / NOE long range total count: 537 / NOE medium range total count: 186 / NOE sequential total count: 440 / Protein phi angle constraints total count: 84 / Protein psi angle constraints total count: 83
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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