[English] 日本語
Yorodumi
- PDB-4cde: Human DPP1 in complex with 4-amino-N-((1S)-1-cyano-2-(4-(4- cyano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cde
TitleHuman DPP1 in complex with 4-amino-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)tetrahydropyran-4-carboxamide
Components(DIPEPTIDYL PEPTIDASE 1 ...Cathepsin C) x 3
KeywordsHYDROLASE / DPP1 / INHIBITOR
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / response to organic substance / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / 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 / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-U6B / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDebreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. ...Debreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Cage, P. / Sanghanee, H. / Breed, J. / Wissler, L.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate.
Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / ...Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / Chohan, K. / Beri, R. / Thong, B. / Wallace, A. / Oreffo, V. / Hutchinson, R. / Harper, S. / Debreczeni, J. / Breed, J. / Wissler, L. / Edman, K.
History
DepositionOct 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Mar 29, 2017Group: Other
Revision 1.3Apr 24, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,13614
Polymers79,4276
Non-polymers1,7098
Water2,558142
1
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5687
Polymers39,7143
Non-polymers8544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-66.5 kcal/mol
Surface area14960 Å2
MethodPISA
2
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5687
Polymers39,7143
Non-polymers8544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-55.8 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.350, 84.350, 224.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
DIPEPTIDYL PEPTIDASE 1 ... , 3 types, 6 molecules ADBECF

#1: Protein DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN / DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I ...DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 13500.163 Da / Num. of mol.: 2 / Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN / Cathepsin C / DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 18630.018 Da / Num. of mol.: 2 / Fragment: DPP1 HEAVY CHAIN, RESIDUES 230-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN / Cathepsin C / DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 7583.444 Da / Num. of mol.: 2 / Fragment: DPP1 LIGHT CHAIN, RESIDUES 371-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I

-
Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 146 molecules

#5: Chemical ChemComp-U6B / 4-AZANYL-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]OXANE-4-CARBOXAMIDE


Mass: 376.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): POSTTRANSLATIONAL MODIFICATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 % / Description: NONE
Crystal growDetails: 21% PEG3350, 200MM AMSO4, 100MM NA ACETATE PH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.97
DetectorDetector: CCD / Date: Feb 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→42.17 Å / Num. obs: 37102 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.88 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.35 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3B

1k3b


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.853 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24174 1851 5 %RANDOM
Rwork0.19359 ---
obs0.19592 35217 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.91 Å20 Å2
2---0.91 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 0 114 142 5727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195803
X-RAY DIFFRACTIONr_bond_other_d0.0010.025175
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9457886
X-RAY DIFFRACTIONr_angle_other_deg0.733.00411861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68123.824272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61215866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6191522
X-RAY DIFFRACTIONr_chiral_restr0.070.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021465
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_it2.0164.3612768
X-RAY DIFFRACTIONr_mcbond_other2.0144.362767
X-RAY DIFFRACTIONr_mcangle_it3.167.3463453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.554.7333034
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 122 -
Rwork0.267 2508 -
obs--99.89 %
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)
12.32950.7982-0.68082.6671-0.51270.88290.0881-0.023-0.555-0.1426-0.2502-0.54120.29030.24860.1620.42650.1513-0.07360.13220.03520.399924.976445.569177.0545
22.29790.14220.1353.2055-0.41930.69230.02870.0661-0.3432-0.23150.10280.70910.2686-0.1419-0.13150.3077-0.115-0.15960.07190.00230.44530.58350.908274.352
31.6551-0.09480.28032.5788-0.29291.89530.0986-0.171-0.33440.22610.06890.79430.238-0.213-0.16750.2501-0.11280.00230.08140.03950.4633-1.964254.073684.2542
44.09851.0151-0.89433.5994-0.67431.85940.05260.8661-0.0722-1.02280.03210.38880.2743-0.3791-0.08470.6890.0465-0.1310.3947-0.06890.060110.890869.098648.1587
52.4085-0.1308-0.17862.5557-0.41880.87290.10650.5354-0.2653-0.6611-0.2398-0.80070.25830.29260.13320.48120.2110.27750.35170.01880.316435.459367.501653.3808
62.3665-0.51020.77894.4616-0.51431.26720.02770.51720.1149-0.619-0.1693-1.00330.02640.42120.14160.34070.0880.30.29610.08560.330938.088877.787554.7702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B206 - 370
3X-RAY DIFFRACTION3C371 - 439
4X-RAY DIFFRACTION4D1 - 119
5X-RAY DIFFRACTION5E206 - 369
6X-RAY DIFFRACTION6F371 - 439

+
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