Schema for PDB Ligand Contacts - Potential contact residues in PDB structures of viral proteins
  Database: wuhCor1    Primary Table: contacts Data last updated: 2020-07-19
Big Bed File: /gbdb/wuhCor1/bbi/contacts.bb
Item Count: 77
Format description: Potential contacts in structures of covid proteins
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart20349Start position of feature on chromosome
chromEnd20655End position of feature on chromosome
name6x1bPDB id _ Residue name + residue number
score25Number of residues in range
strand++ or - for strand
thickStart20349region start
thickEnd20655region end
reserved255fixed 255
blockCount8Number of residue ranges
blockSizes3,3,3,3,3,3,3,6Range sizes
chromStarts0,15,135,141,147,288,294,300residue range start positions
totRes9Number of residues with contacts
allResidueList245,250,290,292,294,341,343,345,346Residues with contacts
allContactsList1,2,2,3,7,1,7,1,1Number of contacts per residue
journal_citation"Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU."Structure citation
journal_authors"(ToBePublished,?,'Kim,Y.','Maltseva,N.','Jedrzejczak,R.','Endres,M.','Chang,C.','Michalska,K.','Joachimiak,A.','CenterforStructuralGenomicsofInfectiousDiseases(CSGID)')"citation authors
_mouseOver"Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU."_mouseOver

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartstotResallResidueListallContactsListjournal_citationjournal_authors_mouseOver
NC_045512v220349206556x1b25+203492065525583,3,3,3,3,3,3,60,15,135,141,147,288,294,3009245,250,290,292,294,341,343,345,3461,2,2,3,7,1,7,1,1"Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.""(ToBePublished,?,'Kim,Y.','Maltseva,N.','Jedrzejczak,R.','Endres,M.','Chang,C.','Michalska,K.','Joachimiak,A.','CenterforStruct ..."Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU."
NC_045512v222561226396wpt35+225612263925563,3,3,3,6,30,15,18,27,33,757334,339,340,343,345,346,3594,2,12,4,10,1,2"Structural and functional analysis of a potent sarbecovirus neutralizing antibody.""(Biorxiv,2020,'Pinto,D.','Park,Y.J.','Beltramello,M.','Walls,A.C.','Tortorici,M.A.','Bianchi,S.','Jaconi,S.','Culap,K.','Zatta, ..."Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state)"
NC_045512v222561228856wps39+2256122885255113,3,3,3,3,3,3,3,3,3,30,3,9,15,18,27,33,36,66,75,32111334,335,337,339,340,343,345,346,356,359,4413,1,1,3,10,3,10,2,4,1,1"Structural and functional analysis of a potent sarbecovirus neutralizing antibody.""(Biorxiv,2020,'Pinto,D.','Park,Y.J.','Beltramello,M.','Walls,A.C.','Tortorici,M.A.','Bianchi,S.','Jaconi,S.','Culap,K.','Zatta, ..."Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment"
NC_045512v222594230116zer48+2259423011255243,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,30,27,30,36,72,90,96,102,105,108,111,114,117,120,123,201,204,246,252,354,357,363,369,41424345,354,355,357,369,375,377,379,380,381,382,383,384,385,386,412,413,427,429,463,464,466,468,4831,1,1,1,4,1,2,2,1,1,1,7,1,5,3,1,1,1,6,1,1,2,2,1"Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient""(ToBePublished,?,'Zhou,D.','Duyvesteyn,H.M.E.','Chen,C.','Huang,C.','Chen,T.','Shih,S.','Lin,Y.','Cheng,C.','Cheng,S.','Huang,Y ..."Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab"
NC_045512v222597230566xdg67+2259723056255103,3,6,3,3,3,6,18,3,30,213,282,294,300,321,327,414,441,45617346,417,440,441,444,446,453,455,456,484,485,486,487,488,489,493,4981,2,6,1,1,7,1,1,4,5,2,8,4,2,16,5,1"Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.""(Science,2020,'Hansen,J.','Baum,A.','Pascal,K.E.','Russo,V.','Giordano,S.','Wloga,E.','Fulton,B.O.','Yan,Y.','Koon,K.','Patel,K ..."Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies"
NC_045512v222597230776lzg60+2259723077255213,3,3,3,3,6,3,3,3,6,3,3,3,3,6,3,3,3,3,9,30,33,213,294,300,309,321,327,333,363,372,387,408,414,420,429,441,450,456,462,47726346,357,417,444,446,449,450,453,455,457,467,468,470,475,482,484,486,487,489,493,496,498,500,501,502,5056,8,1,1,1,3,2,1,2,1,3,1,2,1,1,1,2,6,2,1,1,2,5,3,2,1"Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.""(Cell,2020,'Wang,Q.','Zhang,Y.','Wu,L.','Niu,S.','Song,C.','Zhang,Z.','Lu,G.','Qiao,C.','Hu,Y.','Yuen,K.Y.','Wang,Q.','Zhou,H.' ..."Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2"
NC_045512v222597230776m0j65+2259723077255183,3,3,3,3,6,3,6,6,3,3,3,6,3,3,3,9,30,33,213,294,300,309,321,330,363,372,408,423,429,441,450,456,462,47724346,357,417,444,446,449,450,453,456,457,467,468,470,482,487,489,490,493,496,498,500,501,502,50511,8,1,1,1,5,2,1,1,1,1,1,2,1,2,1,1,10,1,3,4,2,2,2"Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.""(Nature,2020,'Lan,J.','Ge,J.','Yu,J.','Shan,S.','Zhou,H.','Fan,S.','Zhang,Q.','Shi,X.','Wang,Q.','Zhang,L.','Wang,X.')""Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2"
NC_045512v222597230777c0171+2259723077255283,3,3,3,3,3,6,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,30,9,27,33,150,171,186,213,222,225,243,294,300,312,318,327,336,342,354,381,387,414,420,423,429,441,462,47729346,349,355,357,396,403,408,409,417,420,421,427,444,446,450,452,455,458,460,464,473,475,484,486,487,489,493,500,5052,1,3,1,2,3,3,1,2,4,6,1,1,1,7,1,3,1,2,1,3,2,2,2,2,1,1,2,10"A human neutralizing antibody targets the receptor binding site of SARS-CoV-2.""(Nature,2020,'Shi,R.','Shan,C.','Duan,X.','Chen,Z.','Liu,P.','Song,J.','Song,T.','Bi,X.','Han,C.','Wu,L.','Gao,G.','Hu,X.','Zha ..."Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD"
NC_045512v222597231196yz580+2259723119255143,6,3,9,12,3,6,3,6,3,3,3,6,30,75,84,93,108,294,309,330,390,414,420,432,441,51923346,371,372,374,377,378,379,382,383,384,385,444,449,450,456,476,477,484,486,490,493,494,5191,7,3,6,5,2,5,1,5,1,1,1,2,3,1,2,4,6,7,8,5,3,1"H11-D4 complex with SARS-CoV-2 RBD""(ToBePublished,?,'Naismith,J.H.')""H11-D4 complex with SARS-CoV-2 RBD"
NC_045512v222621231136yz778+2262123113255233,3,3,3,6,3,3,3,3,3,3,3,3,3,6,3,3,3,3,3,3,3,30,3,45,48,54,63,69,81,87,96,153,162,222,228,285,306,330,342,390,408,414,420,48925354,355,369,370,372,373,375,377,381,383,386,405,408,428,430,449,450,456,464,468,484,490,492,494,5174,5,3,1,1,1,1,6,3,4,3,4,3,6,2,7,3,1,1,1,6,5,3,2,2"Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2""(ToBePublished,2020,'Naismith,J.H.')""H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex"

PDB Ligand Contacts (contacts) Track Description
 

Description

This track shows potential contact residues for ligands, inferred from structures in the PDB database by Alastair Fyfe, UCSC.

Display Conventions and Configuration

Genomic locations of contact residues are highlighted with thick blocks, that look identical to exons. Contact residues of the same PDB structure are connected by thin intron lines.

To display the 3D structure viewer with these contact residues highlighted, follow the outlink at the top of the details page of any feature.

Methods

PDB SEQRES protein sequences were aligned to the genome with tblastn. Ligands were determined manually, all amino acids closer than 3.5 Angstroms were obtained as described below. The positions of these close amino acids on the genome were determined using the tblastn alignment and are highlighted on the genome with exon blocks.

The find nearby amino acids, inter-atom distances were calculated with the libraries GEMMI and Clipper at a threshold of 3.5 . Distances between atoms whose proximity is due to crystal packing or symmetry are listed but cannot be inspected in the viewer. These contacts are flagged by a check in the "Symm?" column. They include atoms in adjacent unit cells and atoms brought into proximity by application of a symmetry transformation to the asymmetric unit (ASU), but not atoms related by non-crystallographic symmetry (NCS).

For each amino acid in the contact table the "Codon" column gives the codon's nucleotide values and position in the NC_045512.2 reference sequence. Amino acids that could not be aligned to the reference, for example insertions or deletions engineered to facilitate protein expression, are flagged by "-".

Data Access

The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/contacts.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

Track created by Alastair Fyfe, UCSC, mentored by David Haussler.