[English] 日本語
Yorodumi
- PDB-7kkh: P1A4 Fab in complex with ARS1620 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kkh
TitleP1A4 Fab in complex with ARS1620
Components
  • P1A4 Fab Heavy Chain
  • P1A4 Fab Light Chain
KeywordsIMMUNE SYSTEM / ANTITUMOR PROTEIN / Fab / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-91S
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasu, K. / Rohweder, P.J. / Zhang, Z. / Bohn, M.-F. / Shokat, K. / Craik, C.S.
CitationJournal: Cancer Cell / Year: 2022
Title: A covalent inhibitor of K-Ras(G12C) induces MHC class I presentation of haptenated peptide neoepitopes targetable by immunotherapy.
Authors: Zhang, Z. / Rohweder, P.J. / Ongpipattanakul, C. / Basu, K. / Bohn, M.F. / Dugan, E.J. / Steri, V. / Hann, B. / Shokat, K.M. / Craik, C.S.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P1A4 Fab Light Chain
B: P1A4 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6825
Polymers46,2032
Non-polymers4793
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-48 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.782, 71.302, 86.793
Angle α, β, γ (deg.)90.000, 90.657, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Antibody P1A4 Fab Light Chain


Mass: 22329.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody P1A4 Fab Heavy Chain


Mass: 23873.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-91S / (S)-1-{4-[6-chloro-8-fluoro-7-(2-fluoro-6-hydroxyphenyl)quinazolin-4-yl] piperazin-1-yl}propan-1-one


Mass: 432.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19ClF2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70 % MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2→58.77 Å / Num. obs: 42846 / % possible obs: 99.42 % / Redundancy: 10.2 % / Biso Wilson estimate: 34.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.75
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 4212 / CC1/2: 0.49

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZN, 2B0S

5gzn

2b0s


Resolution: 2→58.77 Å / SU ML: 0.2109 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 2128 4.99 %
Rwork0.1852 40554 -
obs0.1862 42682 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.08 Å2
Refinement stepCycle: LAST / Resolution: 2→58.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 32 237 3517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853363
X-RAY DIFFRACTIONf_angle_d1.04524591
X-RAY DIFFRACTIONf_chiral_restr0.0672511
X-RAY DIFFRACTIONf_plane_restr0.0061583
X-RAY DIFFRACTIONf_dihedral_angle_d17.37941183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28651310.29172653X-RAY DIFFRACTION97.27
2.05-2.10.29161410.26832691X-RAY DIFFRACTION98.74
2.1-2.150.31551290.25352681X-RAY DIFFRACTION99.05
2.15-2.220.28281420.24482657X-RAY DIFFRACTION99.33
2.22-2.290.26411330.22922711X-RAY DIFFRACTION99.16
2.29-2.370.24431410.22442682X-RAY DIFFRACTION99.33
2.37-2.470.23861440.21842683X-RAY DIFFRACTION99.68
2.47-2.580.22521550.21282693X-RAY DIFFRACTION99.58
2.58-2.710.24351330.2012713X-RAY DIFFRACTION99.65
2.71-2.880.20521650.20112708X-RAY DIFFRACTION99.93
2.88-3.110.22271310.19162706X-RAY DIFFRACTION99.79
3.11-3.420.19481280.17372719X-RAY DIFFRACTION99.89
3.42-3.910.17721710.16442718X-RAY DIFFRACTION99.83
3.91-4.930.14511460.13662732X-RAY DIFFRACTION99.72
4.93-58.770.20281380.17422807X-RAY DIFFRACTION99.66

+
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