2OBD | Genus

Total Genus 137

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	137
sequence length	472
structure length	472
Chain Sequence	TSHEAGIVCRITKPALLVLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKSIDVSIQDVSVVFKGTLKYGYTTAWWLGIDQSIDFEIDSAIDLQINTQLTADSGRVRTDAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFVQTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKDVSEDLPLPTFSPTLLGDSRMLYFWFSERVFHSLAKVAFQDGRLMLSLMGDEFKAVLETWGFNTNQEIFQEVVGGFPSQAQVTVHCLKMPKISCQNKGVVVDSSVMVKFLFPRPDQQHSVAYTFEEDIVTTVQASYSKKKLFLSLLDFQITPKTVSNLTESSSESIQSFLQSMITAVGIPEVMSRLEVVFTALMNSKGVSLFDIINPEIITRDGFLLLQMDFGFPEHLLVDFLQSLS

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

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The Resolver thinks Pdb

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Time for openFile(/file/5cfd5f6bd84f7d86633eb211/pdb.gz): 1088 ms

reading 472 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

472 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 32 ms

Adding embedded #jmolscript: select ({0:471});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Lipid transport
source organism	Homo sapiens
publication title	Crystal structure of cholesteryl ester transfer protein reveals a long tunnel and four bound lipid molecules. pubmed doi rcsb
molecule keywords	Cholesteryl ester transfer protein
total genus	137
structure length	472
sequence length	472
ec nomenclature
pdb deposition date	2006-12-18

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01273	LBP_BPI_CETP	LBP / BPI / CETP family, N-terminal domain
A	PF02886	LBP_BPI_CETP_C	LBP / BPI / CETP family, C-terminal domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.15.10.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein; domain 1	Bactericidal permeability-increasing protein; domain 1	2obdA02
3.15.20.10	Alpha Beta	Super Roll	Bactericidal permeability-increasing protein; domain 2	Bactericidal permeability-increasing protein; domain 2	2obdA01

2OBDA 1BP1A 1EWFA 5I7JA 5I7LA 3ZPMA 4KGHA 4M4DA 4EWSA 4F2AA 5I7KA 4KGOA
chains in the Genus database with same CATH superfamily

1BP1A 3H4ZA 3UV1A 5I7JA 3E8TA 4F2AA 1USUB 4G0SA 4KGOA 5I7LA 3E8WA 4M4DA 4EWSA 3AOSA 1USVB 3L6IA 3A1ZA 2RCKA 3AOTA 2RQFA 2OBDA 1EWFA 3ZPMA 4KGHA 3N72A 5I7KA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2OBD A;  1BP1 A;  1EWF A;  5I7J A;  5I7L A;  3ZPM A;  4KGH A;  4M4D A;  4EWS A;  4F2A A;  5I7K A;  4KGO A; 
#chains in the Genus database with same CATH topology
 1BP1 A;  3H4Z A;  3UV1 A;  5I7J A;  3E8T A;  4F2A A;  1USU B;  4G0S A;  4KGO A;  5I7L A;  3E8W A;  4M4D A;  4EWS A;  3AOS A;  1USV B;  3L6I A;  3A1Z A;  2RCK A;  3AOT A;  2RQF A;  2OBD A;  1EWF A;  3ZPM A;  4KGH A;  3N72 A;  5I7K A; 
#chains in the Genus database with same CATH homology
 1BP1 A;  3H4Z A;  3UV1 A;  5I7J A;  3E8T A;  4F2A A;  1USU B;  4G0S A;  4KGO A;  5I7L A;  3E8W A;  4M4D A;  4EWS A;  3AOS A;  1USV B;  3L6I A;  3A1Z A;  2RCK A;  3AOT A;  2RQF A;  2OBD A;  1EWF A;  3ZPM A;  4KGH A;  3N72 A;  5I7K A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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2OBDA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations