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- PDB-2p3u: Crystal structure of human factor XA complexed with 3-chloro-N-(4... -

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Entry
Database: PDB / ID: 2p3u
TitleCrystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663}
Components(Coagulation factor X) x 2
KeywordsBLOOD CLOTTING / protein inhibitor complex / coagulation cofactor / protease
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / 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 ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / 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 / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 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-663 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.62 Å
AuthorsAdler, M. / Whitlow, M.
Citation
#1: Journal: Biochemistry / Year: 2002
Title: Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa
Authors: Adler, M. / Kochanny, M.J. / Bin, Y. / Rumennik, G. / Light, D.L. / Biancalana, S. / Whitlow, M.
#2: Journal: TO BE PUBLISHED
Title: Discovery of Highly Potent and Orally Available Thiophene-Anthranilamide-Based Factor Xa Inhibitors
Authors: Ye, B. / Arnaiz, D.O. / Chou, Y.-L. / Griedel, B.D. / Karanjawala, R. / Lee, W. / Morrissey, M.M. / Sacchi, K.L. / Sakata, S.T. / Shaw, K.J. / Wu, S.C. / Zhao, Z. / Adler, M. / Cheeseman, S. ...Authors: Ye, B. / Arnaiz, D.O. / Chou, Y.-L. / Griedel, B.D. / Karanjawala, R. / Lee, W. / Morrissey, M.M. / Sacchi, K.L. / Sakata, S.T. / Shaw, K.J. / Wu, S.C. / Zhao, Z. / Adler, M. / Cheeseman, S. / Dole, W.P. / Ewing, J. / Fitch, R. / Lentz, D. / Liang, A. / Light, D. / Morser, J. / Post, J. / Rumennik, G. / Subramanyam, B. / Sullivan, M.E. / Vergona, R. / Walters, J. / Wang, Y.-X. / White, K.A. / Whitlow, M. / Kochanny, M.J.
#3: Journal: Bioorg.Med.Chem. / Year: 2007
Title: Substituted thiophene-anthranilamides as potent inhibitors of human factor Xa
Authors: Ye, B. / Arnaiz, D.O. / Chou, Y.-L. / Griedel, B.D. / Karanjawala, R. / Lee, W. / Morrissey, M.M. / Sacchi, K.L. / Sakata, S.T. / Shaw, K.J. / Wu, S.C. / Zhao, Z. / Adler, M. / Cheeseman, S. ...Authors: Ye, B. / Arnaiz, D.O. / Chou, Y.-L. / Griedel, B.D. / Karanjawala, R. / Lee, W. / Morrissey, M.M. / Sacchi, K.L. / Sakata, S.T. / Shaw, K.J. / Wu, S.C. / Zhao, Z. / Adler, M. / Cheeseman, S. / Dole, W.P. / Ewing, J. / Fitch, R. / Lentz, D. / Liang, A. / Light, D. / Morser, J. / Post, J. / Rumennik, G. / Subramanyam, B. / Sullivan, M.E. / Vergona, R. / Walters, J. / Wang, Y.-X. / White, K.A. / Whitlow, M. / Kochanny, M.J.
#4: Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: Structure-activity relationships of substituted benzothiophene-anthranilamide factor Xa inhibitors
Authors: Kochanny, M.J. / Adler, M. / Ewing, J. / Griedel, B.D. / Ho, E. / Karanjawala, R. / Lee, W. / Lentz, D. / Liang, A.M. / Morrissey, M.M. / Phillips, G.B. / Post, J. / Sakata, K.L. / ...Authors: Kochanny, M.J. / Adler, M. / Ewing, J. / Griedel, B.D. / Ho, E. / Karanjawala, R. / Lee, W. / Lentz, D. / Liang, A.M. / Morrissey, M.M. / Phillips, G.B. / Post, J. / Sakata, K.L. / Subramanyam, B. / Vergona, R. / Walters, J. / White, K.A. / Whitlow, M. / Ye, B. / Zhao, Z. / Shaw, K.J.
#5: Journal: Biochemistry / Year: 2000
Title: Preparation, Characterization and the Crystal Structure of the Inhibitor ZK-807834 (Ci-1031) Complexed with Factor Xa
Authors: Chou, Y.L. / Davey, D.D. / Eagen, K.A. / Griedel, B.D. / Karanjawala, R. / Phillips, G.B. / Sacchi, K.L. / Shaw, K.J. / Wu, S.C. / Lentz, D. / Liang, A.M. / Trinh, L. / Morrissey, M.M. / Kochanny, M.J.
#6: Journal: J.Med.Chem. / Year: 2000
Title: Crystal Structures of Human Factor Xa Complexed with Potent Inhibitors
Authors: Adler, M. / Davey, D.D. / Phillips, G.B. / Kim, S.H. / Jancarik, J. / Rumennik, G. / Light, D.L. / Whitlow, M.
#7: Journal: J.Med.Chem. / Year: 1998
Title: Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5-Difluoro- 6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4-Yl]-N-Methylglycine (Zk-807834): A Potent, Selective, ...Title: Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5-Difluoro- 6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy]Pyridin-4-Yl]-N-Methylglycine (Zk-807834): A Potent, Selective, and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa
Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A.M. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J.M. / Shaw, K. ...Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A.M. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J.M. / Shaw, K.J. / Smith, D. / Subramanyam, B. / Sullivan, M.E. / Trinh, L. / Vergona, R. / Walters, J. / White, K. / Whitlow, M. / Wu, S. / Xu, W. / Morrissey, M.M.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor X
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5665
Polymers31,9352
Non-polymers6313
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.014, 71.717, 78.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). FACTOR XA FORMS A COMPLEX WITH FACTOR VA IN THE PRESENCE OF CALCIUM AND A PHOSPHOLIPID MEMBRANE TO PRODUCE THE PROTHROMBINASE COMPLEX. THIS ENTRY CONTAINS THE EPIDERMAL GROWTH FACTOR LIKE DOMAIN 2(L) AND THE CATALYTIC DOMAIN (A) OF FACTOR XA IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE COORDINATES DO NOT CONTAIN THE GLA DOMAIN OR THE EPIDERMAL GROWTH FACTOR LIKE DOMAIN 1 OF FACTOR XA. ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A FUNCTIONAL PROTEASE, IT DOES HAVE THE SAME SPECIFICITY AS THE PROTHROMBINASE COMPLEX. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, L BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: EGF-like 2 domain / Source method: isolated from a natural source / Details: EXTRACTED FROM BLOOD / Source: (natural) Homo sapiens (human) / References: UniProt: P00742
#2: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 26346.000 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-663 / 3-CHLORO-N-(4-CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL)AMINO]CARBONYL}-6-METHOXYPHENYL)-4-[(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE


Mass: 550.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18Cl3N5O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5
Details: A THREE-FOLD EXCESS OF 3-Chloro-4-(2-methylamino-imidazol-1-ylmethyl)-thiophene-2-carboxylic acid [4-chloro-2-(5-chloro-pyridin-2-ylcarbamoyl)-6-methoxy-phenyl]-amide WAS ADDED TO THE DES- ...Details: A THREE-FOLD EXCESS OF 3-Chloro-4-(2-methylamino-imidazol-1-ylmethyl)-thiophene-2-carboxylic acid [4-chloro-2-(5-chloro-pyridin-2-ylcarbamoyl)-6-methoxy-phenyl]-amide WAS ADDED TO THE DES-GLA-FACTOR XA. THE PROTEIN WAS THEN CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500 AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 20 MM NACL, 25 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION) WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE DAYS, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2000
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.62→20 Å / Num. obs: 40439 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.04 / Net I/σ(I): 18.4
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.392 / % possible all: 97.9

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Processing

Software
NameClassification
CNXrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB Entry 1FJS

1fjs


Resolution: 1.62→19.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1261609.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1569 3.9 %RANDOM
Rwork0.191 ---
obs0.192 39893 97.2 %-
all-40430 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2348 Å2 / ksol: 0.38301 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---5.12 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.62→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 37 267 2524
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.652
X-RAY DIFFRACTIONc_mcangle_it2.532.5
X-RAY DIFFRACTIONc_scbond_it2.462.5
X-RAY DIFFRACTIONc_scangle_it3.693.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.62-1.720.28012113.30.251162110.019615995.3
1.72-1.850.22912650.21086245
1.85-2.040.21322580.18846327
2.04-2.330.24152790.18966421
2.33-2.940.22112690.19476524
2.94-19.80.18662883.30.180462116648
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2water_rep.parwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4663.par663.top

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