[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Journal, issue, pagesNat Commun, Vol. 12, Page 4848-4848, Year 2021
Publish dateSep 16, 2020 (structure data deposition date)
AuthorsNewman, J.A. / Douangamath, A. / Yadzani, S. / Yosaatmadja, Y. / Aimon, A. / Brandao-Neto, J. / Dunnett, L. / Gorrie-Stone, T. / Skyner, R. / Fearon, D. ...Newman, J.A. / Douangamath, A. / Yadzani, S. / Yosaatmadja, Y. / Aimon, A. / Brandao-Neto, J. / Dunnett, L. / Gorrie-Stone, T. / Skyner, R. / Fearon, D. / Schapira, M. / von Delft, F. / Gileadi, O.
External linksNat Commun / PubMed:34381037
MethodsX-ray diffraction
Resolution1.788 - 3.04 Å
Structure data

PDB-5rl6:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z198195770
Method: X-RAY DIFFRACTION / Resolution: 1.921 Å

PDB-5rl7:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z364321922
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-5rl8:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53825177
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-5rl9:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1703168683
Method: X-RAY DIFFRACTION / Resolution: 1.788 Å

PDB-5rlb:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z216450634
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-5rlc:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z56923284
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-5rld:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z19735981
Method: X-RAY DIFFRACTION / Resolution: 2.233 Å

PDB-5rle:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1429867185
Method: X-RAY DIFFRACTION / Resolution: 2.268 Å

PDB-5rlf:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z235341991
Method: X-RAY DIFFRACTION / Resolution: 2.235 Å

PDB-5rlg:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z19739650
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5rlh:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434778
Method: X-RAY DIFFRACTION / Resolution: 2.379 Å

PDB-5rli:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z45617795
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

PDB-5rlj:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1407673036
Method: X-RAY DIFFRACTION / Resolution: 1.879 Å

PDB-5rlk:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1509882419
Method: X-RAY DIFFRACTION / Resolution: 1.956 Å

PDB-5rll:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z425387594
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-5rlm:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1650168321
Method: X-RAY DIFFRACTION / Resolution: 1.858 Å

PDB-5rln:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z364328788
Method: X-RAY DIFFRACTION / Resolution: 2.147 Å

PDB-5rlo:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1454310449
Method: X-RAY DIFFRACTION / Resolution: 2.097 Å

PDB-5rlp:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z166605480
Method: X-RAY DIFFRACTION / Resolution: 2.562 Å

PDB-5rlq:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 2.225 Å

PDB-5rlr:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z822382694
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

PDB-5rls:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z59181945
Method: X-RAY DIFFRACTION / Resolution: 2.278 Å

PDB-5rlt:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53116498
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-5rlu:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z744754722
Method: X-RAY DIFFRACTION / Resolution: 2.347 Å

PDB-5rlv:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2467208649
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-5rlw:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z45705015
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5rly:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2027049478
Method: X-RAY DIFFRACTION / Resolution: 2.434 Å

PDB-5rlz:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2293643386
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5rm0:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1492796719
Method: X-RAY DIFFRACTION / Resolution: 1.909 Å

PDB-5rm1:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z426041412
Method: X-RAY DIFFRACTION / Resolution: 1.896 Å

PDB-5rm2:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1741964527
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-5rm3:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1745658474
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-5rm4:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1639162606
Method: X-RAY DIFFRACTION / Resolution: 2.96 Å

PDB-5rm5:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z373768900
Method: X-RAY DIFFRACTION / Resolution: 2.06 Å

PDB-5rm6:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z396380540
Method: X-RAY DIFFRACTION / Resolution: 2.128 Å

PDB-5rm7:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z69118333
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-5rm8:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1614545742
Method: X-RAY DIFFRACTION / Resolution: 2.143 Å

PDB-5rm9:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434942
Method: X-RAY DIFFRACTION / Resolution: 2.076 Å

PDB-5rma:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z321318226
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-5rmb:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434920
Method: X-RAY DIFFRACTION / Resolution: 2.206 Å

PDB-5rmc:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z24758179
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-5rmd:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z57614330
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-5rme:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z26333434
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-5rmf:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z54226006
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-5rmg:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285675722
Method: X-RAY DIFFRACTION / Resolution: 2.115 Å

PDB-5rmh:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1101755952
Method: X-RAY DIFFRACTION / Resolution: 2.021 Å

PDB-5rmi:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53860899
Method: X-RAY DIFFRACTION / Resolution: 2.116 Å

PDB-5rmj:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z68299550
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5rmk:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1273312153
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-5rml:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-5rmm:
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with POB0066
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-6zsl:
Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7nio:
Crystal structure of the SARS-CoV-2 helicase APO form
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-7nn0:
Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP
Method: X-RAY DIFFRACTION / Resolution: 3.04 Å

PDB-7nng:
Crystal structure of the SARS-CoV-2 helicase in complex with Z2327226104
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-LJA:
N-[3-(carbamoylamino)phenyl]acetamide

ChemComp-HOH:
WATER

ChemComp-VVD:
5-(acetylamino)-2-fluorobenzoic acid

ChemComp-VVG:
N-(2-fluorophenyl)ethanesulfonamide

ChemComp-UR7:
1-(3-fluoro-4-methylphenyl)methanesulfonamide

ChemComp-VVJ:
N-cycloheptyl-N-methylmethanesulfonamide

ChemComp-VVM:
4-amino-N-phenylbenzene-1-sulfonamide

ChemComp-VVY:
2-phenoxy-1-(pyrrolidin-1-yl)ethan-1-one

ChemComp-VVP:
4-methoxy-1H-indole

ChemComp-NY7:
N-(2-methoxy-5-methylphenyl)glycinamide

ChemComp-VW1:
(2S)-2-(4-cyanophenoxy)propanamide

ChemComp-K2P:
2-(trifluoromethoxy)benzoic acid

ChemComp-JFM:
N-(2-phenylethyl)methanesulfonamide

ChemComp-VW4:
(2S)-2-phenylpropane-1-sulfonamide

ChemComp-NYV:
1-(propan-2-yl)-1H-imidazole-4-sulfonamide

ChemComp-H04:
1-(2-ethoxyphenyl)piperazine

ChemComp-VW7:
N-(8-methyl-1,2,3,4-tetrahydroquinolin-5-yl)acetamide

ChemComp-NZG:
3-(acetylamino)-4-fluorobenzoic acid

ChemComp-UQS:
N-[(2-fluorophenyl)methyl]-1H-pyrazol-4-amine

ChemComp-VWA:
(1S)-1-(4-fluorophenyl)-N-methylethan-1-amine

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-VWD:
(1R)-2-(methylsulfonyl)-1-phenylethan-1-ol

ChemComp-VWG:
N-hydroxyquinoline-2-carboxamide

ChemComp-UVJ:
3-(2-methyl-1H-benzimidazol-1-yl)propanamide

ChemComp-JG4:
2-(thiophen-2-yl)-1H-imidazole

ChemComp-VWJ:
N-(propan-2-yl)-1H-benzimidazol-2-amine

ChemComp-S9S:
~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide

ChemComp-K34:
5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole

ChemComp-VWM:
(3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid

ChemComp-S7G:
~{N}-[(3~{R})-1,2,3,4-tetrahydroquinolin-3-yl]ethanamide

ChemComp-RY4:
N-[4-(aminomethyl)phenyl]methanesulfonamide

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol

ChemComp-S7J:
2-(trifluoromethyl)pyrimidine-5-carboxamide

ChemComp-PK4:
2-fluoro-N,3-dimethylbenzene-1-sulfonamide

ChemComp-NUA:
N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide

ChemComp-HR5:
~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide

ChemComp-N0E:
~{N}-(4-hydroxyphenyl)-3-phenyl-propanamide

ChemComp-GQJ:
methyl (2~{S},4~{R})-1-(furan-2-ylcarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylate

ChemComp-EJQ:
~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide

ChemComp-JHJ:
N-(4-methoxyphenyl)-N'-pyridin-4-ylurea

ChemComp-VWV:
ethyl (1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)acetate

ChemComp-6SU:
methyl 3-(methylsulfonylamino)benzoate

ChemComp-VWY:
N-ethyl-4-[(methylsulfonyl)amino]benzamide

ChemComp-RYM:
4-(benzimidazol-1-ylmethyl)benzenecarbonitrile

ChemComp-NX7:
(2,6-difluorophenyl)(pyrrolidin-1-yl)methanone

ChemComp-MUK:
4,6-dimethyl-~{N}-phenyl-pyrimidin-2-amine

ChemComp-VX4:
[(4S)-4-methylazepan-1-yl](1,3-thiazol-4-yl)methanone

ChemComp-STV:
~{N}-(1,3-benzodioxol-5-ylmethyl)ethanesulfonamide

ChemComp-JOV:
3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide

ChemComp-O2A:
N-methyl-1H-indole-7-carboxamide

ChemComp-VXD:
N-(3-chloro-2-methylphenyl)glycinamide

ChemComp-VXG:
(3S,4R)-1-acetyl-4-phenylpyrrolidine-3-carboxylic acid

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-UJK:
1-(2-methylphenyl)-1,2,3-triazole-4-carboxylic acid

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HYDROLASE / SARS-CoV-2 Helicase NSP13 / NSP13 / Helicase / SARS-CoV-2

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more