[English] 日本語
Yorodumi
- PDB-4e7r: Thrombin in complex with 3-amidinophenylalanine inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e7r
TitleThrombin in complex with 3-amidinophenylalanine inhibitor
Components
  • Hirudin variant-2
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE / KRINGLE / HYDROLASE / BLOOD COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / GLYCOSYLATION / BLOOD
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-0NW / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRuehmann, E. / Heine, A. / Klebe, G.
CitationJournal: MEDCHEMCOMM / Year: 2012
Title: New 3-amidinophenylalanine-derived inhibitors of matriptase
Authors: Hammami, M. / Ruehmann, E. / Mauerer, M. / Heine, A. / Guetschow, M. / Klebe, G. / Steinmetzer, T.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Mar 13, 2013Group: Other
Revision 1.3Aug 17, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 6, 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
L: Thrombin light chain
M: Thrombin light chain
H: Thrombin heavy chain
G: Thrombin heavy chain
I: Hirudin variant-2
J: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,94219
Polymers70,7376
Non-polymers2,20613
Water4,774265
1
L: Thrombin light chain
H: Thrombin heavy chain
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51710
Polymers35,3683
Non-polymers1,1497
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-37 kcal/mol
Surface area12260 Å2
MethodPISA
2
M: Thrombin light chain
G: Thrombin heavy chain
J: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4259
Polymers35,3683
Non-polymers1,0576
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-38 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.242, 50.284, 71.837
Angle α, β, γ (deg.)97.61, 96.61, 90.57
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'H' and (resseq 16:60F or resseq 60I: 146 or resseq 150:244 )
211chain 'G' and (resseq 1016:1060 or resseq 1060I:1146 or resseq 1150:1244 )

-
Components

-
Protein/peptide , 2 types, 4 molecules LMIJ

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1491.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945

-
Protein / Sugars , 2 types, 4 molecules HG

#2: Protein Thrombin heavy chain


Mass: 29780.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 5 types, 276 molecules

#5: Chemical ChemComp-0NW / 3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide


Mass: 602.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H33Cl2N5O3S
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 277.15 K / pH: 7.5
Details: 15% PEG8000, 20MM SODIUM PHOSPHATE, 175MM SODIUM CHLORIDE, PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54178
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2011
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.246→29.3 Å / Num. obs: 32856 / % possible obs: 95.6 % / Observed criterion σ(I): 13.4 / Redundancy: 2.7 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.4

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8D

1h8d


Resolution: 2.25→29.26 Å / SU ML: 0.74 / σ(F): 1.97 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1590 5.07 %
Rwork0.171 --
obs0.174 31385 95.1 %
all-32856 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0916 Å23.2049 Å2-6.8074 Å2
2---2.6107 Å2-3.0964 Å2
3---2.7023 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 140 265 5004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114926
X-RAY DIFFRACTIONf_angle_d1.1686680
X-RAY DIFFRACTIONf_dihedral_angle_d16.8051873
X-RAY DIFFRACTIONf_chiral_restr0.079698
X-RAY DIFFRACTIONf_plane_restr0.004839
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H1933X-RAY DIFFRACTIONPOSITIONAL
12G1933X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.246-2.31880.36841500.28512483X-RAY DIFFRACTION88
2.3188-2.40170.25061360.21492705X-RAY DIFFRACTION94
2.4017-2.49780.26931350.19512694X-RAY DIFFRACTION95
2.4978-2.61140.25851300.18882697X-RAY DIFFRACTION95
2.6114-2.7490.25061810.18042674X-RAY DIFFRACTION95
2.749-2.92110.26641330.17572735X-RAY DIFFRACTION96
2.9211-3.14640.23311570.1742752X-RAY DIFFRACTION96
3.1464-3.46260.21071390.16562724X-RAY DIFFRACTION97
3.4626-3.96250.21471270.16062756X-RAY DIFFRACTION96
3.9625-4.98840.16211540.12312774X-RAY DIFFRACTION98
4.9884-29.26170.19321480.1782801X-RAY DIFFRACTION98
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)
13.3062-1.37220.91092.280.50961.59450.09980.0813-0.42860.0755-0.11640.12190.2239-0.0075-0.04270.0709-0.02480.00320.1224-0.03950.08932.09212.93715.8746
22.73930.0915-0.80640.61620.76451.45050.08670.7694-0.0718-0.2609-0.2022-0.0154-0.1788-0.0614-0.02190.11810.01730.02220.32050.00630.177616.10511.261511.5202
31.6779-0.09460.42780.57510.34450.91840.00420.66450.0644-0.16340.1014-0.1654-0.11370.3747-0.04620.12510.00090.01560.35350.01610.158814.367613.0279.5816
41.9740.20380.66391.0446-0.48021.34250.04180.1412-0.045-0.0701-0.07440.00530.06350.05170.050.07350.043-0.00270.1399-0.01920.11036.06129.06921.1425
57.6174-3.8608-0.21114.71220.36618.25220.298-0.2533-0.31970.0790.2097-0.0175-0.0657-0.2345-0.48630.1882-0.0158-0.04510.21430.02710.101116.58963.144838.7808
62.5054-0.51891.19942.01490.31732.05260.0481-0.2015-0.24840.0254-0.0057-0.18950.08290.0720.02510.13570.0485-0.06680.12460.03610.179314.35750.740631.3011
72.19-1.1279-0.51832.24720.11651.68190.1090.17380.0223-0.0414-0.0886-0.0631-0.0255-0.0795-0.02410.0873-0.01660.00020.11540.00360.06825.46498.276625.463
82.1901-0.64780.4386.8212-2.33272.73810.05790.05940.12360.0235-0.0818-0.0646-0.0840.1050.02870.03780.0045-0.00680.1242-0.03920.227213.299615.091925.8399
91.76690.1378-0.66470.71070.37711.1995-0.0256-0.1154-0.25290.30960.0488-0.27380.35240.211-0.1860.21940.0079-0.13560.1048-0.02340.1437-4.3361-7.474-11.2982
100.4575-0.0110.25681.72210.22030.91260.0072-0.0625-0.05140.55060.00230.07520.2166-0.05810.00310.24010.00460.02020.0846-0.00630.1276-14.3963-12.9023-11.8619
113.4744-0.4804-3.51477.10550.52453.62830.07490.12240.1047-0.9020.11580.4041-0.0487-0.2307-0.2620.32440.0323-0.10260.23290.02390.1994-17.9525-3.4237-34.4651
120.67330.1662-0.89831.84750.43821.44160.0499-0.1296-0.09060.17130.0969-0.59190.33160.33880.1070.14250.0488-0.01460.1345-0.02410.2428-0.3692-6.4305-21.9985
133.2472-1.4002-1.06192.11531.43011.53820.00710.13840.0568-0.64060.064-0.3945-0.12160.0078-0.06220.28470.01560.12160.23930.01560.1434-5.6052-16.5356-38.5473
142.4770.00410.0970.69370.17122.36870.08360.04290.0403-0.21620.0023-0.40770.15840.21990.15620.13440.03640.08750.1651-0.08580.2967-2.1002-14.5542-31.2513
151.64020.17340.20812.3343-0.0261.8018-0.04680.0416-0.2437-0.13220.0314-0.10830.040.06680.01150.1248-0.0080.01540.086-0.00910.1298-10.1124-9.0738-26.2329
163.81272.4122-0.06844.6232-3.95474.94110.1195-0.43820.07470.39770.10840.7698-0.2971-1.3968-0.2270.22880.00190.16060.4163-0.06320.5433-29.5746-12.3733-17.5788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain H and resid 16:33 )H16 - 33
2X-RAY DIFFRACTION2( chain H and resid 34:60E )H34 - 60E
3X-RAY DIFFRACTION3( chain H and resid 60F:97A )H60F - 97A
4X-RAY DIFFRACTION4( chain H and resid 98:162 )H98 - 162
5X-RAY DIFFRACTION5( chain H and resid 163:170 )H163 - 170
6X-RAY DIFFRACTION6( chain H and resid 171:191 )H171 - 191
7X-RAY DIFFRACTION7( chain H and resid 192:220 )H192 - 220
8X-RAY DIFFRACTION8( chain H and resid 221:246 )H221 - 247
9X-RAY DIFFRACTION9( chain G and resid 1016:1041 )G1016 - 1041
10X-RAY DIFFRACTION10( chain G and resid 1042:1124 )G1042 - 1124
11X-RAY DIFFRACTION11( chain G and resid 1125:1131 )G1125 - 1131
12X-RAY DIFFRACTION12( chain G and resid 1132:1162 )G1132 - 1162
13X-RAY DIFFRACTION13( chain G and resid 1163:1170 )G1163 - 1170
14X-RAY DIFFRACTION14( chain G and resid 1171:1191 )G1171 - 1191
15X-RAY DIFFRACTION15( chain G and resid 1192:1237 )G1192 - 1237
16X-RAY DIFFRACTION16( chain G and resid 1238:1245 )G1238 - 1247

+
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