2OK4 | Genus

Total Genus 28

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	28
Knots found	KnotProt 2.0: K
sequence length	110
structure length	109
Chain Sequence	EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPISIGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGLA

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/5cfd61b0d84f7d86633eb2db/pdb.gz): 1021 ms

reading 109 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

109 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:108});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

publication title	New insights into the reductive half-reaction mechanism of aromatic amine dehydrogenase revealed by reaction with carbinolamine substrates. pubmed doi rcsb
molecule keywords	Aromatic amine dehydrogenase, small subunit
molecule tags	Oxidoreductase
total genus	28
structure length	109
sequence length	110
chains with identical sequence	H
other databases	KnotProt 2.0: K
ec nomenclature	ec 1.4.9.2: Aralkylamine dehydrogenase (azurin).
pdb deposition date	2007-01-16

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF02975	Me-amine-dh_L	Methylamine dehydrogenase, L chain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	2ok4D00

2HJ4D 2I0TD 1MDAL 2OK4D 2H47B 3SVWC 2AGWD 3RN0C 2J55L 1MAEL 3SWSC 4L3HC 2I0SD 2AGXD 3L4MC 2HJBD 3RMZC 3RLMC 3ORVC 3L4OC 3PXSC 4FAVC 2AH0D 4FB1C 2IUVD 2IUPD 2AGZD 1MAFL 2OIZD 4Y5RC 4L3GC 4FA9C 4FANC 3SJLC 2MADL 4K3IC 4FA4C 4FA5C 2H3XB 2Q7QD 2AGYD 1MG2B 2AGLD 2IURD 2IUQD 2OK6D 2OJYD 3SLEC 2J57K 2HXCD 3C75L 3PXWC 1MG3B 2AH1D 4L1QC 2I0RD 2J56L 3SXTC 2GC4B 2BBKL 2HKMD 2GC7B 2HKRD 3PXTC 2MTAL 4O1QC 3RN1C 4FA1C 2IAAB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2HJ4 D;  2I0T D;  1MDA L;  2OK4 D;  2H47 B;  3SVW C;  2AGW D;  3RN0 C;  2J55 L;  1MAE L;  3SWS C;  4L3H C;  2I0S D;  2AGX D;  3L4M C;  2HJB D;  3RMZ C;  3RLM C;  3ORV C;  3L4O C;  3PXS C;  4FAV C;  2AH0 D;  4FB1 C;  2IUV D;  2IUP D;  2AGZ D;  1MAF L;  2OIZ D;  4Y5R C;  4L3G C;  4FA9 C;  4FAN C;  3SJL C;  2MAD L;  4K3I C;  4FA4 C;  4FA5 C;  2H3X B;  2Q7Q D;  2AGY D;  1MG2 B;  2AGL D;  2IUR D;  2IUQ D;  2OK6 D;  2OJY D;  3SLE C;  2J57 K;  2HXC D;  3C75 L;  3PXW C;  1MG3 B;  2AH1 D;  4L1Q C;  2I0R D;  2J56 L;  3SXT C;  2GC4 B;  2BBK L;  2HKM D;  2GC7 B;  2HKR D;  3PXT C;  2MTA L;  4O1Q C;  3RN1 C;  4FA1 C;  2IAA B; 
#chains in the Genus database with same CATH topology
 2HJ4 D;  2I0T D;  1MDA L;  2OK4 D;  2H47 B;  3SVW C;  2AGW D;  3RN0 C;  2J55 L;  1MAE L;  3SWS C;  4L3H C;  2I0S D;  2AGX D;  3L4M C;  2HJB D;  3RMZ C;  3RLM C;  3ORV C;  3L4O C;  3PXS C;  4FAV C;  2AH0 D;  4FB1 C;  2IUV D;  2IUP D;  2AGZ D;  1MAF L;  2OIZ D;  4Y5R C;  4L3G C;  4FA9 C;  4FAN C;  3SJL C;  2MAD L;  4K3I C;  4FA4 C;  4FA5 C;  2H3X B;  2Q7Q D;  2AGY D;  1MG2 B;  2AGL D;  2IUR D;  2IUQ D;  2OK6 D;  2OJY D;  3SLE C;  2J57 K;  2HXC D;  3C75 L;  3PXW C;  1MG3 B;  2AH1 D;  4L1Q C;  2I0R D;  2J56 L;  3SXT C;  2GC4 B;  2BBK L;  2HKM D;  2GC7 B;  2HKR D;  3PXT C;  2MTA L;  4O1Q C;  3RN1 C;  4FA1 C;  2IAA B; 
#chains in the Genus database with same CATH homology
 2HJ4 D;  2I0T D;  1MDA L;  2OK4 D;  2H47 B;  3SVW C;  2AGW D;  3RN0 C;  2J55 L;  1MAE L;  3SWS C;  4L3H C;  2I0S D;  2AGX D;  3L4M C;  2HJB D;  3RMZ C;  3RLM C;  3ORV C;  3L4O C;  3PXS C;  4FAV C;  2AH0 D;  4FB1 C;  2IUV D;  2IUP D;  2AGZ D;  1MAF L;  2OIZ D;  4Y5R C;  4L3G C;  4FA9 C;  4FAN C;  3SJL C;  2MAD L;  4K3I C;  4FA4 C;  4FA5 C;  2H3X B;  2Q7Q D;  2AGY D;  1MG2 B;  2AGL D;  2IUR D;  2IUQ D;  2OK6 D;  2OJY D;  3SLE C;  2J57 K;  2HXC D;  3C75 L;  3PXW C;  1MG3 B;  2AH1 D;  4L1Q C;  2I0R D;  2J56 L;  3SXT C;  2GC4 B;  2BBK L;  2HKM D;  2GC7 B;  2HKR D;  3PXT C;  2MTA L;  4O1Q C;  3RN1 C;  4FA1 C;  2IAA B;

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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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2OK4D

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations