[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

TitleUse of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Journal, issue, pagesSci Rep, Vol. 10, Page 21964-21964, Year 2020
Publish dateApr 28, 2020 (structure data deposition date)
AuthorsChowdhury, R. / Abboud, M.I. / McAllister, T.E. / Banerji, B. / Bhushan, B. / Sorensen, J.L. / Kawamura, A. / Schofield, C.J.
External linksSci Rep / PubMed:33319810
MethodsX-ray diffraction
Resolution1.46 - 2.279 Å
Structure data

PDB-6yvw:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic BB-328
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-6yvx:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic BB-287
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6yvz:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic JLS-367
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-6yw0:
Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-6yw1:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-6yw2:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic FG2216 and RaPID-derived cyclic peptide 3C (14-mer)
Method: X-RAY DIFFRACTION / Resolution: 2.14 Å

PDB-6yw3:
HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer)
Method: X-RAY DIFFRACTION / Resolution: 2.279 Å

PDB-6yw4:
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Method: X-RAY DIFFRACTION / Resolution: 1.528 Å

Chemicals

ChemComp-FE:
Unknown entry

ChemComp-PW5:
4-[(5-bromanyl-4,6-dimethyl-pyridin-2-yl)amino]-4-oxidanylidene-butanoic acid

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-MN:
Unknown entry

ChemComp-2JP:
4-(isoquinolin-3-ylamino)-4-oxobutanoic acid

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

ChemComp-PW8:
4-[(5-bromanylisoquinolin-3-yl)amino]-4-oxidanylidene-butanoic acid

ChemComp-AKG:
2-OXOGLUTARIC ACID

ChemComp-UN9:
N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

ChemComp-OGA:
N-OXALYLGLYCINE / inhibitor*YM

ChemComp-SO4:
SULFATE ION

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX

+
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://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 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