[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

TitleGroup deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2
Journal, issue, pagesTo Be Published
Publish dateOct 15, 2024 (structure data deposition date)
AuthorsSaini, M. / Chopra, A. / Aschenbrenner, J.C. / Marples, P.G. / Balcomb, B.H. / Fearon, D. / von Delft, F. / Ruiz, F.X. / Arnold, E.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.56 - 2.43 Å
Structure data

PDB-7hkb:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z438067480 (DNV2_NS5A-x0135)
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7hkc:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z4628744292 (DNV2_NS5A-x0160)
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-7hkd:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z53825479 (DNV2_NS5A-x0172)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hke:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z53860899 (DNV2_NS5A-x0174)
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7hkf:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z55669204 (DNV2_NS5A-x0191)
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-7hkg:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z56953052 (DNV2_NS5A-x0210)
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7hkh:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z68299550 (DNV2_NS5A-x0248)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7hki:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z68639747 (DNV2_NS5A-x0250)
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7hkj:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z71580604 (DNV2_NS5A-x0254)
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7hkk:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z802824098 (DNV2_NS5A-x0279)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hkl:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z818928496 (DNV2_NS5A-x0283)
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7hkm:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z851110644 (DNV2_NS5A-x0288)
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7hkn:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z952016136 (DNV2_NS5A-x0323)
Method: X-RAY DIFFRACTION / Resolution: 2.43 Å

PDB-7hko:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z106579662 (DNV2_NS5A-x0376)
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-7hkp:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1198279205 (DNV2_NS5A-x0414)
Method: X-RAY DIFFRACTION / Resolution: 2.12 Å

PDB-7hkq:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1203329531 (DNV2_NS5A-x0428)
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-7hkr:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1262617180 (DNV2_NS5A-x0471)
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7hks:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z198194394 (DNV2_NS5A-x0612)
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-7hkt:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1983897532 (DNV2_NS5A-x0615)
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-7hku:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z291279160 (DNV2_NS5A-x0741)
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-7hkv:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z300245038 (DNV2_NS5A-x0749)
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7hkw:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z329734230 (DNV2_NS5A-x0789)
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7hkx:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z3765495818 (DNV2_NS5A-x0825)
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-7hky:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z383325512 (DNV2_NS5A-x0829)
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7hkz:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with POB0029 (DNV2_NS5A-x0851)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hl0:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with NCL-00023818 (DNV2_NS5A-x0963)
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-7hl1:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z3241250482 (DNV2_NS5A-x1037)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hl2:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z3219959731 (DNV2_NS5A-x1046)
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7hl3:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z1741972704 (DNV2_NS5A-x1073)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7hl4:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with HL11 (DNV2_NS5A-x1094)
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hl5:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z44548882 (DNV2_NS5A-x1149)
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7hl6:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z31113727 (DNV2_NS5A-x1192)
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7hl7:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z48978335 (DNV2_NS5A-x1196)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hl8:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z57157143 (DNV2_NS5A-x1212)
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7hl9:
Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z53833304 (DNV2_NS5A-x1217)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-PO4:
PHOSPHATE ION

PDB-1am1:
ATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE

ChemComp-HOH:
WATER

ChemComp-CL:
Unknown entry

PDB-1ap7:
P19-INK4D FROM MOUSE, NMR, 20 STRUCTURES

ChemComp-8BT:
N-cyclopentylmethanesulfonamide

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

PDB-1bdl:
HIV-1 (2:31-37) PROTEASE COMPLEXED WITH INHIBITOR SB203386

PDB-1bdk:
AN NMR, CD, MOLECULAR DYNAMICS, AND FLUOROMETRIC STUDY OF THE CONFORMATION OF THE BRADYKININ ANTAGONIST B-9340 IN WATER AND IN AQUEOUS MICELLAR SOLUTIONS

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

ChemComp-TEK:
~{N}-(1-ethylbenzimidazol-2-yl)ethanamide

ChemComp-LQV:
(2S)-N-(5-methylpyridin-2-yl)oxolane-2-carboxamide

PDB-1bdj:
COMPLEX STRUCTURE OF HPT DOMAIN AND CHEY

ChemComp-LJR:
1-cyclohexyl-N-methylmethanesulfonamide

ChemComp-K24:
N,2-dimethyl-1,3-thiazole-5-carboxamide


ChemComp, No image

ChemComp-KBU:
Unknown entry

ChemComp-NUY:
[4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone

PDB-1bdi:
PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

PDB-1bdh:
PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX

PDB-1bdf:
STRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE ALPHA SUBUNIT N-TERMINAL DOMAIN

ChemComp-O1M:
4-(4-fluorophenyl)piperazine-1-carboxamide

ChemComp-WMS:
5-fluoro-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyridin-3-amine

ChemComp-LV4:
1-[2-(trifluoromethyloxy)phenyl]thiourea

ChemComp-O0P:
N-[(3-fluorophenyl)methyl]-N-methylsulfuric diamide

PDB-1aqb:
RETINOL-BINDING PROTEIN (RBP) FROM PIG PLASMA

PDB-1amz:
CHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE

ChemComp-UV7:
N-[(1H-pyrazol-4-yl)methyl]acetamide

PDB-1bdg:
HEXOKINASE FROM SCHISTOSOMA MANSONI COMPLEXED WITH GLUCOSE

ChemComp-PYZ:
4-IODOPYRAZOLE

ChemComp-HV2:
1,1-bis(oxidanylidene)thietan-3-ol

ChemComp-W3G:
pyridazin-3(2H)-one

ChemComp-HOW:
1,2-oxazol-3-amine

PDB-1bdm:
THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY

ChemComp-0XM:
1,1-diphenylmethanamine

PDB-1ajs:
REFINEMENT AND COMPARISON OF THE CRYSTAL STRUCTURES OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE AND ITS COMPLEX WITH 2-METHYLASPARTATE

PDB-1bdn:
CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT

PDB-1bdo:
STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD PHASING

ChemComp-T6R:
1-ethyl-1H-benzimidazole

Source
  • dengue virus type 2
KeywordsVIRAL PROTEIN / Diamond Light Source / Rutgers University / I04-1 / READDI / Dengue Virus / crystallographic fragment screening / PanDDA / XChemExplorer

+
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