[English] 日本語
Yorodumi
- PDB-5vph: CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vph
TitleCRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1
Components
  • Der p 1 allergen
  • FAB 4C1 - HEAVY CHAIN
  • FAB 4C1 - LIGHT CHAIN
KeywordsHYDROLASE/IMMUNE SYSTEM / DER P 1 / ALLERGEN-ANTIBODY COMPLEX / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


peptidase 1 (mite) / cysteine-type peptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidase 1 / Der p 1 allergen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens.
Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 3RVX
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_PDB_id_code / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Der p 1 allergen
C: FAB 4C1 - LIGHT CHAIN
D: FAB 4C1 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7325
Polymers76,6303
Non-polymers1022
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-30 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.109, 59.377, 236.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Der p 1 allergen


Mass: 25014.805 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 81-302 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides pteronyssinus (European house dust mite)
References: UniProt: Q3HWZ5, UniProt: P08176*PLUS

-
Antibody , 2 types, 2 molecules CD

#2: Antibody FAB 4C1 - LIGHT CHAIN


Mass: 23937.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)
#3: Antibody FAB 4C1 - HEAVY CHAIN


Mass: 27677.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)

-
Non-polymers , 3 types, 202 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M HEPES, 10% W/V PEG4000, 0.05M GLYGLYGLY, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23380 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 24.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.596 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F5V, 3RVV

3f5v

3rvv
PDB Unreleased entry


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.939 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1194 5.1 %RANDOM
Rwork0.178 ---
obs0.18 22108 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--1.84 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 5 200 5243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225176
X-RAY DIFFRACTIONr_bond_other_d0.0060.023403
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9417062
X-RAY DIFFRACTIONr_angle_other_deg0.88538282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92623.913230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41815794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0351528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.53220
X-RAY DIFFRACTIONr_mcbond_other0.131.51303
X-RAY DIFFRACTIONr_mcangle_it1.05425218
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86931956
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9034.51844
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 81 -
Rwork0.231 1344 -
obs--79.39 %
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)
11.6668-0.13160.30921.2921-0.47041.8687-0.073-0.0856-0.16160.08260.0903-0.00480.21770.0574-0.01730.06120.05210.03770.16420.13910.0994-21.4220.3428.172
22.7335-0.99740.23022.2875-0.22776.46630.08510.1792-0.0724-0.2931-0.04970.0298-0.2216-0.7183-0.03540.0739-0.0406-0.01250.21820.06850.0343-32.6479.255-28.774
38.0026-2.7068-1.5693.36471.24254.13540.11250.9450.1781-0.40530.109-0.11650.119-0.0349-0.22150.2533-0.07990.00910.230.0604-0.0067-22.96812.656-63.837
42.36870.1943-0.47491.24750.33953.36160.07090.0109-0.2309-0.0485-0.0045-0.0770.26270.1799-0.06640.09090.0026-0.00050.06930.04930.0549-13.7561.141-25.821
52.9663-1.91910.40257.0337-2.30784.01990.10630.36020.5551-0.13370.0588-0.5792-0.13950.3549-0.16520.0894-0.09080.05610.1483-0.00820.1612-9.40614.611-54.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 222
2X-RAY DIFFRACTION2C1 - 104
3X-RAY DIFFRACTION3C105 - 211
4X-RAY DIFFRACTION4D1 - 119
5X-RAY DIFFRACTION5D120 - 220

+
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