[English] 日本語
Yorodumi
- PDB-7jy3: Structure of HbA with compound 23 (PF-07059013) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jy3
TitleStructure of HbA with compound 23 (PF-07059013)
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / hemoglobin
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / OXYGEN MOLECULE / Chem-VUD / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsJasti, J.
CitationJournal: J.Med.Chem. / Year: 2021
Title: PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease.
Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, ...Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, X. / France, S.P. / Howard, R.M. / Janz, J.M. / Jasti, J. / Jasuja, R. / Jones, L.H. / King-Ahmad, A. / Knee, K.M. / Kohrt, J.T. / Limberakis, C. / Liras, S. / Martinez, C.A. / McClure, K.F. / Narayanan, A. / Narula, J. / Novak, J.J. / O'Connell, T.N. / Parikh, M.D. / Piotrowski, D.W. / Plotnikova, O. / Robinson, R.P. / Sahasrabudhe, P.V. / Sharma, R. / Thuma, B.A. / Vasa, D. / Wei, L. / Wenzel, A.Z. / Withka, J.M. / Xiao, J. / Yayla, H.G.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,72719
Polymers62,0814
Non-polymers4,64615
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-108 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 82.470, 65.080
Angle α, β, γ (deg.)90.000, 99.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871

-
Non-polymers , 5 types, 407 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H24O6
#6: Chemical ChemComp-VUD / 6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)pyridin-2(1H)-one


Mass: 365.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16FN5O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M lithium sulfate, 30-32% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→44.68 Å / Num. obs: 55793 / % possible obs: 96.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/av σ(I): 11.3 / Net I/σ(I): 11.3
Reflection shellResolution: 1.48→1.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 496 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3WHM

3whm


Resolution: 1.48→29.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2775 4.97 %RANDOM
Rwork0.18 ---
obs0.181 55793 60.5 %-
Displacement parametersBiso max: 106.1 Å2 / Biso mean: 26.28 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.4548 Å20 Å20.6565 Å2
2--0.297 Å20 Å2
3---2.1578 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.48→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 324 392 5100
Biso mean--23.83 37.13 -
Num. residues----574
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1577SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes886HARMONIC5
X-RAY DIFFRACTIONt_it4872HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion570SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5872SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4872HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6653HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.85
LS refinement shellResolution: 1.48→1.49 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2087 5 6.67 %
Rwork-70 -
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.96410.0620.12310.8834-0.13880.6371-0.09130.4946-0.5297-0.12650.0681-0.06280.05190.0510.0232-0.1497-0.03570.0347-0.0782-0.1545-0.067814.5781-11.824431.2918
23.2134-0.0531-0.05230.99820.10170.4266-0.07260.44670.1571-0.00910.07450.0499-0.07-0.0245-0.0018-0.1194-0.0307-0.0106-0.05410.0181-0.1278-2.47835.52630.8483
31.71690.03490.15070.4408-0.12310.3123-0.01-0.2598-0.29310.05540.00350.03350.0125-0.0780.0065-0.17150.00140.0128-0.14160.059-0.086-0.1483-10.966458.2574
42.56190.36450.26331.26950.17740.8808-0.0405-0.11760.1922-0.0687-0.01340.0522-0.0741-0.00450.0539-0.18490.0019-0.0012-0.1864-0.0227-0.15116.95046.536157.4769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 141
2X-RAY DIFFRACTION2{ B|* }B1 - 146
3X-RAY DIFFRACTION3{ C|* }C1 - 141
4X-RAY DIFFRACTION4{ D|* }D1 - 146

+
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