[English] 日本語
Yorodumi
- PDB-7u64: Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u64
TitleCrystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl
Components(HY6-F9.6 Fab ...) x 2
KeywordsIMMUNE SYSTEM / mAb / opioid
Function / homologyChem-7V7 / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRodarte, J.V. / Pancera, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Structure / Year: 2023
Title: Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding.
Authors: Rodarte, J.V. / Baehr, C. / Hicks, D. / Liban, T.L. / Weidle, C. / Rupert, P.B. / Jahan, R. / Wall, A. / McGuire, A.T. / Strong, R.K. / Runyon, S. / Pravetoni, M. / Pancera, M.
History
DepositionMar 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HY6-F9.6 Fab heavy chain
B: HY6-F9.6 Fab light chain
C: HY6-F9.6 Fab heavy chain
D: HY6-F9.6 Fab light chain
E: HY6-F9.6 Fab heavy chain
F: HY6-F9.6 Fab light chain
G: HY6-F9.6 Fab heavy chain
H: HY6-F9.6 Fab light chain
I: HY6-F9.6 Fab heavy chain
J: HY6-F9.6 Fab light chain
K: HY6-F9.6 Fab heavy chain
L: HY6-F9.6 Fab light chain
M: HY6-F9.6 Fab heavy chain
N: HY6-F9.6 Fab light chain
O: HY6-F9.6 Fab heavy chain
P: HY6-F9.6 Fab light chain
Q: HY6-F9.6 Fab heavy chain
R: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,946100
Polymers435,11318
Non-polymers6,83482
Water50,9642829
1
A: HY6-F9.6 Fab heavy chain
B: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,33214
Polymers48,3462
Non-polymers98612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-37 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: HY6-F9.6 Fab heavy chain
D: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7645
Polymers48,3462
Non-polymers4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-38 kcal/mol
Surface area19240 Å2
MethodPISA
3
E: HY6-F9.6 Fab heavy chain
F: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,08311
Polymers48,3462
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-39 kcal/mol
Surface area19250 Å2
MethodPISA
4
G: HY6-F9.6 Fab heavy chain
H: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,28315
Polymers48,3462
Non-polymers93713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-57 kcal/mol
Surface area19000 Å2
MethodPISA
5
I: HY6-F9.6 Fab heavy chain
J: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02410
Polymers48,3462
Non-polymers6788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-56 kcal/mol
Surface area19270 Å2
MethodPISA
6
K: HY6-F9.6 Fab heavy chain
L: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,08311
Polymers48,3462
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-35 kcal/mol
Surface area19260 Å2
MethodPISA
7
M: HY6-F9.6 Fab heavy chain
N: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8005
Polymers48,3462
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-28 kcal/mol
Surface area19170 Å2
MethodPISA
8
O: HY6-F9.6 Fab heavy chain
P: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20113
Polymers48,3462
Non-polymers85511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-47 kcal/mol
Surface area19280 Å2
MethodPISA
9
Q: HY6-F9.6 Fab heavy chain
R: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,37816
Polymers48,3462
Non-polymers1,03214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-45 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.139, 218.139, 89.023
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31

-
Components

-
Antibody , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR

#1: Antibody
HY6-F9.6 Fab heavy chain


Mass: 24345.039 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
HY6-F9.6 Fab light chain


Mass: 24000.818 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 2911 molecules

#3: Chemical
ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide


Mass: 336.471 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2829 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M Sodium Acetate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97388 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97388 Å / Relative weight: 1
ReflectionResolution: 1.75→43.33 Å / Num. obs: 475987 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.068 / Rrim(I) all: 0.155 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.7851.3234820.7890.4420.99898.8
9.59-43.335.328.428820.9990.020.04798.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEX

4lex


Resolution: 1.75→43.33 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 23982 5.04 %
Rwork0.1972 451470 -
obs0.1986 475452 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30132 0 475 2829 33436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006331263
X-RAY DIFFRACTIONf_angle_d0.896242486
X-RAY DIFFRACTIONf_chiral_restr0.0584770
X-RAY DIFFRACTIONf_plane_restr0.00665414
X-RAY DIFFRACTIONf_dihedral_angle_d13.764911097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.31158110.283815101X-RAY DIFFRACTION99.19
1.77-1.790.31248530.272614841X-RAY DIFFRACTION98.77
1.79-1.810.29287900.259514901X-RAY DIFFRACTION98.72
1.81-1.840.27747240.252615072X-RAY DIFFRACTION99.54
1.84-1.860.30538040.245814960X-RAY DIFFRACTION98.58
1.86-1.890.26758360.244115032X-RAY DIFFRACTION99.52
1.89-1.910.2648340.239114984X-RAY DIFFRACTION99.21
1.91-1.940.29177460.238414995X-RAY DIFFRACTION98.99
1.94-1.970.2517810.219715170X-RAY DIFFRACTION99.58
1.97-20.23857480.204414930X-RAY DIFFRACTION99.39
2-2.040.24678680.214985X-RAY DIFFRACTION99.22
2.04-2.070.24897360.21415111X-RAY DIFFRACTION99.3
2.07-2.110.25097850.198815069X-RAY DIFFRACTION99.69
2.11-2.160.21988010.189815018X-RAY DIFFRACTION99.7
2.16-2.20.21198510.189515084X-RAY DIFFRACTION99.51
2.2-2.260.23288100.195815028X-RAY DIFFRACTION99.6
2.26-2.310.23467880.187515052X-RAY DIFFRACTION99.65
2.31-2.380.22418140.189715044X-RAY DIFFRACTION99.65
2.38-2.440.23258600.190415070X-RAY DIFFRACTION99.61
2.44-2.520.23997650.198215003X-RAY DIFFRACTION99.6
2.52-2.610.2477300.201815290X-RAY DIFFRACTION99.86
2.61-2.720.24188880.20514982X-RAY DIFFRACTION99.78
2.72-2.840.24227190.203415217X-RAY DIFFRACTION99.93
2.84-2.990.22237600.199915093X-RAY DIFFRACTION99.88
2.99-3.180.22298470.193115123X-RAY DIFFRACTION99.85
3.18-3.420.20357920.179415112X-RAY DIFFRACTION99.84
3.43-3.770.18528240.164215063X-RAY DIFFRACTION99.96
3.77-4.310.16828210.159215060X-RAY DIFFRACTION99.89
4.31-5.430.16988140.160715076X-RAY DIFFRACTION99.49
5.43-43.330.23487820.219815004X-RAY DIFFRACTION99.11

+
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