[English] 日本語
Yorodumi
- PDB-3ekt: Crystal Structure of the inhibitor Darunavir (DRV) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ekt
TitleCrystal Structure of the inhibitor Darunavir (DRV) in complex with a multi-drug resistant HIV-1 protease variant (L10F/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation.)
ComponentsProtease
KeywordsHYDROLASE / HIV-1 / protease / multi-drug resistance / Darunavir / AIDS
Function / homology
Function and homology information


RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-017 / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsPrabu-Jeyabalan, M. / King, N.M. / Bandaranayake, R.M.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.
Authors: King, N.M. / Prabu-Jeyabalan, M. / Bandaranayake, R.M. / Nalam, M.N. / Nalivaika, E.A. / Ozen, A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 25, 2012Group: Data collection / Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.5Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease
B: Protease
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30619
Polymers43,2634
Non-polymers2,04315
Water5,783321
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3566
Polymers21,6322
Non-polymers7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-35 kcal/mol
Surface area9030 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,94913
Polymers21,6322
Non-polymers1,31811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-67 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.013, 92.013, 106.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Protease / / Retropepsin / PR


Mass: 10815.788 Da / Num. of mol.: 4 / Fragment: UNP residues 491-589 / Mutation: Q7K,L10I,G48V,I54V,V64I, V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017 / Darunavir


Mass: 547.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Refer citation, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→40 Å / Num. all: 34578 / Num. obs: 34578 / % possible obs: 95.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.766 / SU ML: 0.133 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1713 5 %RANDOM
Rwork0.209 ---
obs0.211 34447 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.77 Å2 / Biso mean: 13.827 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 133 321 3402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223295
X-RAY DIFFRACTIONr_bond_other_d0.0010.023170
X-RAY DIFFRACTIONr_angle_refined_deg1.122.0284521
X-RAY DIFFRACTIONr_angle_other_deg1.0637350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76125104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02585
X-RAY DIFFRACTIONr_nbd_refined0.1950.3549
X-RAY DIFFRACTIONr_nbd_other0.2240.33229
X-RAY DIFFRACTIONr_nbtor_refined0.1810.51561
X-RAY DIFFRACTIONr_nbtor_other0.0870.51851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5374
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1820.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.539
X-RAY DIFFRACTIONr_mcbond_it0.8971.52673
X-RAY DIFFRACTIONr_mcbond_other0.1161.5858
X-RAY DIFFRACTIONr_mcangle_it0.98723363
X-RAY DIFFRACTIONr_scbond_it1.71131370
X-RAY DIFFRACTIONr_scangle_it2.4244.51158
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 151 -
Rwork0.215 2400 -
all-2551 -
obs--97 %
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)
12.894-0.19323.97751.18711.29977.55320.17060.1286-0.14120.04850.0075-0.03010.22290.1672-0.1781-0.07310.0054-0.007-0.05750.0027-0.063122.8694-35.421635.5564
22.02250.67364.24334.03641.67599.28720.1575-0.0708-0.1550.15830.0531-0.11730.30830.0062-0.2106-0.0588-0.0026-0.0022-0.1023-0.0034-0.070919.2128-37.525935.2454
316.70125.7972-3.33472.5708-1.17731.45710.13680.29970.17550.0949-0.03730.1890.0031-0.0039-0.0994-0.0915-0.0276-0.0033-0.00070.0152-0.069116.5673-26.106930.8624
412.26810.3004-2.52849.523-2.32240.56660.19930.03670.32520.262-0.22450.1219-0.0944-0.07170.0252-0.0279-0.04840.0172-0.0592-0.007-0.051714.3363-27.379839.9495
54.6007-4.04380.85163.5622-0.353820.06320.12810.37530.05270.087-0.1807-0.1141-0.3508-0.35890.0525-0.1461-0.0037-0.04220.0226-0.0152-0.02286.0024-16.456227.0424
60.5979-1.64360.02094.63521.577622.77310.06650.06640.05510.2829-0.01490.1955-0.5157-0.2968-0.0516-0.0017-0.0757-0.0401-0.1132-0.0249-0.045611.0356-13.376243.4069
721.6544-9.41939.20499.0381-10.034615.47910.46040.1458-0.3804-0.0836-0.04260.08570.2072-0.7042-0.4177-0.0793-0.09290.0121-0.0443-0.0315-0.139919.4115-26.417716.8184
86.35290.1302-3.368517.57995.62038.48030.0854-0.0503-0.20220.374-0.0027-0.2024-0.49520.3885-0.0826-0.1437-0.0484-0.0199-0.00380.0303-0.145313.1811-29.987253.9893
914.5014-6.86194.96169.4153-4.257911.0026-0.41530.8981-0.4274-0.34970.0789-0.15280.83530.09430.3364-0.0144-0.09360.071-0.1116-0.0215-0.025923.0795-31.877217.3412
105.83974.51251.5369.20492.72968.63870.3144-0.8123-0.27930.1465-0.8145-0.38370.22270.30270.5001-0.1708-0.0238-0.00280.02640.10930.006216.0479-35.893853.4542
118.1682-1.601-0.68722.0504-1.35481.84040.12710.08810.93120.103-0.1864-0.4485-0.1313-0.37310.0593-0.1008-0.0130.0089-0.03110.080.008915.2999-19.036425.4039
125.44540.3186-0.41887.3944-0.79551.2452-0.00550.21370.18970.2430.01790.8797-0.31630.106-0.0124-0.074-0.03760.0786-0.0909-0.0264-0.00348.8339-22.773745.3862
135.3457-5.0818-2.25364.88742.67235.92690.1020.3958-0.0988-0.1745-0.023-0.0761-0.0323-0.0463-0.079-0.0273-0.0481-0.0123-0.02450.0211-0.015215.9039-31.993325.3158
140.948-2.24032.40518.8238-3.86257.0410.0567-0.0212-0.14680.32950.0389-0.28480.01040.0192-0.0957-0.0902-0.02160.01650.0278-0.0075-0.021219.759-29.786445.5326
152.21443.8964-0.432612.4958-5.19743.5740.0424-0.05870.3264-0.2012-0.02560.4193-0.2065-0.381-0.0167-0.12690.0199-0.01730.0045-0.00190.0153.132249.4202-10.1434
169.56418.1082-4.24499.3961-1.75793.22750.0583-0.33860.2050.0438-0.18890.4598-0.335-0.31740.1306-0.0620.0711-0.011-0.080.00350.02584.757752.2701-7.5197
174.52221.33542.63693.70075.62648.64530.1290.1013-0.22720.07090.0868-0.2043-0.0994-0.0218-0.2158-0.02060.0142-0.00280.00070.0193-0.03515.083947.4723-12.6988
181.8829-0.08882.87311.95371.91526.5410.06270.0903-0.0819-0.0863-0.0106-0.2635-0.1009-0.177-0.052-0.02850.01370.0027-0.02460.0152-0.013712.439442.9146-4.9603
193.05482.765-5.4844.4081-8.408216.0718-0.3977-0.2798-0.1082-0.252-0.0187-0.43390.01050.46470.4164-0.10550.0975-0.02840.0077-0.0696-0.002929.622445.4591-11.525
201.61261.9598-4.55288.0992-10.033416.39640.07340.0701-0.32060.044-0.4935-0.40210.36140.14460.4201-0.11020.0944-0.06020.0014-0.061-0.015821.617330.959-5.9849
2131.31213.83334.01310.56424.93527.9667-0.57980.42930.157-0.26190.22950.0413-0.99050.00220.35020.05540.04140.0775-0.18820.0031-0.123618.313456.4986-23.3073
224.0843-6.51270.738145.63036.70698.45210.0771-0.0956-0.13580.6723-0.44880.08540.5678-0.85750.3717-0.1512-0.083-0.0551-0.00980.0604-0.13576.243835.58825.6682
2342.904524.51839.696920.4726-1.834610.6119-0.7322-0.06-0.0811-0.76960.82080.1837-0.9736-0.1301-0.08870.1140.1427-0.0039-0.1331-0.0533-0.087612.052958.453-22.8263
248.4342-5.2094-6.166891.2591.18154.58730.4802-0.1646-0.20561.499-0.3081.13080.4285-0.6834-0.1722-0.1556-0.0696-0.06190.1766-0.0275-0.07481.14240.07815.8561
252.62860.9588-0.04294.26732.01011.04820.124-0.03480.09710.0027-0.0418-0.06540.13320.2402-0.0822-0.0239-0.0008-0.003-0.057-0.032-0.052622.291946.3358-17.935
263.7910.44382.64892.98061.38182.2430.06440.1752-0.0072-0.21650.04460.0650.26430.1775-0.1089-0.02-0.0131-0.0148-0.0321-0.0151-0.06417.022337.22280.2661
272.2881-3.04521.32436.261-0.15281.94010.3740.13950.2691-0.3803-0.0677-0.0258-0.2154-0.0144-0.30630.0385-0.00340.013-0.07980.0098-0.018714.238655.2591-13.8044
289.41841.60850.5440.28810.02910.3360.1301-0.5688-0.32680.06230.17980.19320.2259-0.0316-0.3099-0.0189-0.03510.0032-0.01580.0072-0.02745.280239.7089-3.8502
2917.7671-3.53487.96815.61113.093733.4429-0.2365-0.4319-0.2636-0.5730.4824-0.0076-0.9269-0.4616-0.2459-0.01530.0098-0.0053-0.09060.00450.007412.2388-21.13235.4023
3022.87913.5410.458441.24836.47521.1673-0.18251.03550.220.92960.59650.78250.06510.8535-0.4140.03670.037-0.02180.20420.0582-0.017418.961941.3557-9.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION2B1 - 5
4X-RAY DIFFRACTION2B94 - 99
5X-RAY DIFFRACTION3A22 - 30
6X-RAY DIFFRACTION4B22 - 30
7X-RAY DIFFRACTION5A44 - 57
8X-RAY DIFFRACTION6B44 - 57
9X-RAY DIFFRACTION7A60 - 66
10X-RAY DIFFRACTION8B60 - 66
11X-RAY DIFFRACTION9A68 - 72
12X-RAY DIFFRACTION10B68 - 72
13X-RAY DIFFRACTION11A74 - 85
14X-RAY DIFFRACTION12B74 - 85
15X-RAY DIFFRACTION13A86 - 93
16X-RAY DIFFRACTION14B86 - 93
17X-RAY DIFFRACTION15C1 - 5
18X-RAY DIFFRACTION15C94 - 99
19X-RAY DIFFRACTION16D1 - 5
20X-RAY DIFFRACTION16D94 - 99
21X-RAY DIFFRACTION17C22 - 30
22X-RAY DIFFRACTION18D22 - 30
23X-RAY DIFFRACTION19C44 - 57
24X-RAY DIFFRACTION20D44 - 57
25X-RAY DIFFRACTION21C60 - 66
26X-RAY DIFFRACTION22D60 - 66
27X-RAY DIFFRACTION23C68 - 72
28X-RAY DIFFRACTION24D68 - 72
29X-RAY DIFFRACTION25C74 - 85
30X-RAY DIFFRACTION26D74 - 85
31X-RAY DIFFRACTION27C86 - 93
32X-RAY DIFFRACTION28D86 - 93
33X-RAY DIFFRACTION29D - P200
34X-RAY DIFFRACTION30Q200

+
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