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PDBe specifications


Unique identifier OMICS_07431
Name PDBe
Alternative name Protein Data Bank in Europe
Restrictions to use None
Data access File download, Browse, Application programming interface
Maintained Yes


  • person_outline Sameer Velankar

Publications for Protein Data Bank in Europe

PDBe citations


Structure and mechanism of the two component α helical pore forming toxin YaxAB

Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] tal 2D class averages using EMAN2, imposing C10 symmetry and using 5° rotational steps. FSC between the model and the final map was computed using an online tool based on EMAN2 (https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/), which revealed an agreement between map and model up to a resolution of 6.6 Å (FSC = 0.5). […]


Self homodimerization of an actinoporin by disulfide bridging reveals implications for their structure and pore formation

Sci Rep
PMCID: 5920107
PMID: 29700324
DOI: 10.1038/s41598-018-24688-2
call_split See protocol

[…] e (http://www.pymol.org). The geometrical characterization of StI W111C homodimer protein-protein interfaces was carryout with PDBePISA web server in Protein Data Bank in Europe (http://www.ebi.ac.uk/pdbe/pisa/). […]


Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding

PMCID: 5923319
PMID: 29649119
DOI: 10.3390/toxins10040153

[…] ion interface calculations for HcA2 with SV2C (6ES1) was generated using the ‘Protein interfaces, surfaces and assemblies’ service PISA at the European Bioinformatics Institute. (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html) [,,].Structural sequence alignment. Structure based sequence alignment of HcA1 (Chain B from 4JRA) [] and HcA2 (Chain A from 6ES1) binding to SV2C-L4 was generated using PD […]


Caveat Usor: Assessing Differences between Major Chemistry Databases

PMCID: 5900829
PMID: 29451740
DOI: 10.1002/cmdc.201700724

[…] urces submit all the heteroatom structures (HETATM). These encompass resolved small molecules including salts and reagents. Secondly, there are four different sources within wwPDB and the NCBI. While PDBe and PDBj counts are more or less concordant at 25 057 and 25 252, respectively, RCSB PDB drops slightly to 24 140. It is not clear which of these sets was loaded into CS on the 25th of May, but U […]


The H subunit of the restriction endonuclease CglI contains a prototype DEAD Z1 helicase like motor

Nucleic Acids Res
PMCID: 5861437
PMID: 29471489
DOI: 10.1093/nar/gky107

[…] fined with phenix.refine.1.8.3 (). TLS groups were determined by TLSMD server (http://skuld.bmsc.washington.edu/∼tlsmd/) (). The crystal contacts were analysed using PISA server (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html) (). Electrostatic surface potential was calculated using PDB2PQR and APBS (,). All molecular scale representations were prepared using the PyMOL Molecular Graphics System ( […]


Schistosoma mansoni SmKI 1 serine protease inhibitor binds to elastase and impairs neutrophil function and inflammation

PLoS Pathog
PMCID: 5823468
PMID: 29425229
DOI: 10.1371/journal.ppat.1006870
call_split See protocol

[…] d. Analysis of the predicted protein-protein interface was performed with the “Protein interfaces, surfaces and assemblies” service PISA at the European Bioinformatics Institute (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html) to calculate interactions and interface properties []. The complex was also manually analyzed with the software Pymol. […]


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PDBe institution(s)
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, UK; InterPro, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Genome Campus, Hinxton, UK; CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
PDBe funding source(s)
Supported by Wellcome Trust [104948]; UK Biotechnology and Biological Sciences Research Council [BB/M011674/1, BB/N019172/1, BB/M020347/1]; European Union [284209]; European Molecular Biology Laboratory (EMBL).

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