Schema for PDB Ligand Contacts - Potential contact residues in PDB structures of viral proteins
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Database: wuhCor1 Primary Table: contacts Data last updated: 2020-07-19
Big Bed File Download: /gbdb/wuhCor1/bbi/contacts.bb Item Count: 77 The data is stored in the binary BigBed format.
Format description: Potential contacts in structures of covid proteins
field | example | description |
chrom | NC_045512v2 | Reference sequence chromosome or scaffold | chromStart | 20349 | Start position of feature on chromosome | chromEnd | 20655 | End position of feature on chromosome | name | 6x1b | PDB id _ Residue name + residue number | score | 25 | Number of residues in range | strand | + | + or - for strand | thickStart | 20349 | region start | thickEnd | 20655 | region end | reserved | 255 | fixed 255 | blockCount | 8 | Number of residue ranges | blockSizes | 3,3,3,3,3,3,3,6 | Range sizes | chromStarts | 0,15,135,141,147,288,294,300 | residue range start positions | totRes | 9 | Number of residues with contacts | allResidueList | 245,250,290,292,294,341,343,345,346 | Residues with contacts | allContactsList | 1,2,2,3,7,1,7,1,1 | Number 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 |
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Sample Rows
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chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | totRes | allResidueList | allContactsList | journal_citation | journal_authors | _mouseOver |
NC_045512v2 | 20349 | 20655 | 6x1b | 25 | + | 20349 | 20655 | 255 | 8 | 3,3,3,3,3,3,3,6 | 0,15,135,141,147,288,294,300 | 9 | 245,250,290,292,294,341,343,345,346 | 1,2,2,3,7,1,7,1,1 | "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_045512v2 | 22561 | 22639 | 6wpt | 35 | + | 22561 | 22639 | 255 | 6 | 3,3,3,3,6,3 | 0,15,18,27,33,75 | 7 | 334,339,340,343,345,346,359 | 4,2,12,4,10,1,2 | "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_045512v2 | 22561 | 22885 | 6wps | 39 | + | 22561 | 22885 | 255 | 11 | 3,3,3,3,3,3,3,3,3,3,3 | 0,3,9,15,18,27,33,36,66,75,321 | 11 | 334,335,337,339,340,343,345,346,356,359,441 | 3,1,1,3,10,3,10,2,4,1,1 | "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_045512v2 | 22594 | 23011 | 6zer | 48 | + | 22594 | 23011 | 255 | 24 | 3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3 | 0,27,30,36,72,90,96,102,105,108,111,114,117,120,123,201,204,246,252,354,357,363,369,414 | 24 | 345,354,355,357,369,375,377,379,380,381,382,383,384,385,386,412,413,427,429,463,464,466,468,483 | 1,1,1,1,4,1,2,2,1,1,1,7,1,5,3,1,1,1,6,1,1,2,2,1 | "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_045512v2 | 22597 | 23056 | 6xdg | 67 | + | 22597 | 23056 | 255 | 10 | 3,3,6,3,3,3,6,18,3,3 | 0,213,282,294,300,321,327,414,441,456 | 17 | 346,417,440,441,444,446,453,455,456,484,485,486,487,488,489,493,498 | 1,2,6,1,1,7,1,1,4,5,2,8,4,2,16,5,1 | "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_045512v2 | 22597 | 23077 | 6lzg | 60 | + | 22597 | 23077 | 255 | 21 | 3,3,3,3,3,6,3,3,3,6,3,3,3,3,6,3,3,3,3,9,3 | 0,33,213,294,300,309,321,327,333,363,372,387,408,414,420,429,441,450,456,462,477 | 26 | 346,357,417,444,446,449,450,453,455,457,467,468,470,475,482,484,486,487,489,493,496,498,500,501,502,505 | 6,8,1,1,1,3,2,1,2,1,3,1,2,1,1,1,2,6,2,1,1,2,5,3,2,1 | "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_045512v2 | 22597 | 23077 | 6m0j | 65 | + | 22597 | 23077 | 255 | 18 | 3,3,3,3,3,6,3,6,6,3,3,3,6,3,3,3,9,3 | 0,33,213,294,300,309,321,330,363,372,408,423,429,441,450,456,462,477 | 24 | 346,357,417,444,446,449,450,453,456,457,467,468,470,482,487,489,490,493,496,498,500,501,502,505 | 11,8,1,1,1,5,2,1,1,1,1,1,2,1,2,1,1,10,1,3,4,2,2,2 | "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_045512v2 | 22597 | 23077 | 7c01 | 71 | + | 22597 | 23077 | 255 | 28 | 3,3,3,3,3,3,6,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3 | 0,9,27,33,150,171,186,213,222,225,243,294,300,312,318,327,336,342,354,381,387,414,420,423,429,441,462,477 | 29 | 346,349,355,357,396,403,408,409,417,420,421,427,444,446,450,452,455,458,460,464,473,475,484,486,487,489,493,500,505 | 2,1,3,1,2,3,3,1,2,4,6,1,1,1,7,1,3,1,2,1,3,2,2,2,2,1,1,2,10 | "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_045512v2 | 22597 | 23119 | 6yz5 | 80 | + | 22597 | 23119 | 255 | 14 | 3,6,3,9,12,3,6,3,6,3,3,3,6,3 | 0,75,84,93,108,294,309,330,390,414,420,432,441,519 | 23 | 346,371,372,374,377,378,379,382,383,384,385,444,449,450,456,476,477,484,486,490,493,494,519 | 1,7,3,6,5,2,5,1,5,1,1,1,2,3,1,2,4,6,7,8,5,3,1 | "H11-D4 complex with SARS-CoV-2 RBD" | "(ToBePublished,?,'Naismith,J.H.')" | "H11-D4 complex with SARS-CoV-2 RBD" |
NC_045512v2 | 22621 | 23113 | 6yz7 | 78 | + | 22621 | 23113 | 255 | 23 | 3,3,3,3,6,3,3,3,3,3,3,3,3,3,6,3,3,3,3,3,3,3,3 | 0,3,45,48,54,63,69,81,87,96,153,162,222,228,285,306,330,342,390,408,414,420,489 | 25 | 354,355,369,370,372,373,375,377,381,383,386,405,408,428,430,449,450,456,464,468,484,490,492,494,517 | 4,5,3,1,1,1,1,6,3,4,3,4,3,6,2,7,3,1,1,1,6,5,3,2,2 | "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" |
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PDB Ligand Contacts (contacts) Track Description
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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 Å. 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.
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