[English] 日本語
Yorodumi
- PDB-5t1k: Cetuximab Fab in complex with CQFDA(Ph)2STRRLKC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t1k
TitleCetuximab Fab in complex with CQFDA(Ph)2STRRLKC
Components
  • (CETUXIMAB FAB HEAVY ...) x 2
  • CETUXIMAB FAB LIGHT CHAIN
  • CQFDA(PH)2STRRLKC PEPTIDE
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / MESO-ERYTHRITOL / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Oct 4, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
E: CQFDA(PH)2STRRLKC PEPTIDE
F: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,77212
Polymers97,1756
Non-polymers5976
Water9,332518
1
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
E: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8646
Polymers48,5793
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-47 kcal/mol
Surface area19040 Å2
MethodPISA
2
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
F: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9086
Polymers48,5963
Non-polymers3123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-40 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.280, 83.250, 212.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein/peptide , 1 types, 2 molecules EF

#4: Protein/peptide CQFDA(PH)2STRRLKC PEPTIDE


Mass: 1582.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Antibody , 3 types, 4 molecules ACBD

#1: Antibody CETUXIMAB FAB LIGHT CHAIN


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Mus musculus (house mouse)
#2: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23708.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Mus musculus (house mouse)
#3: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23725.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Mus musculus (house mouse)

-
Non-polymers , 3 types, 524 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.5 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, PH 5.5
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→33.2 Å / Num. obs: 41117 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.5
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.7 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.48→33.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.213 2055 5 %
Rwork0.16 --
obs0.163 41103 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.48→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 33 518 7323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087038
X-RAY DIFFRACTIONf_angle_d1.1499581
X-RAY DIFFRACTIONf_dihedral_angle_d13.7952538
X-RAY DIFFRACTIONf_chiral_restr0.0731074
X-RAY DIFFRACTIONf_plane_restr0.0051228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.5340.26291210.20292306X-RAY DIFFRACTION89
2.534-2.59730.27951350.18642560X-RAY DIFFRACTION100
2.5973-2.66750.28581370.17882597X-RAY DIFFRACTION100
2.6675-2.7460.24251340.18272561X-RAY DIFFRACTION100
2.746-2.83450.26051370.18312605X-RAY DIFFRACTION100
2.8345-2.93580.28081370.1792599X-RAY DIFFRACTION100
2.9358-3.05330.25731370.17482596X-RAY DIFFRACTION100
3.0533-3.19210.22261370.17082615X-RAY DIFFRACTION100
3.1921-3.36030.22931370.16672596X-RAY DIFFRACTION100
3.3603-3.57060.2051370.1552606X-RAY DIFFRACTION100
3.5706-3.84590.19361370.15242607X-RAY DIFFRACTION100
3.8459-4.23220.19041400.13822650X-RAY DIFFRACTION100
4.2322-4.8430.15691400.11892662X-RAY DIFFRACTION100
4.843-6.09550.16981410.13962679X-RAY DIFFRACTION100
6.0955-33.19060.20421480.18962809X-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