2J56 | Genus

Total Genus 31

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	31
Knots found	KnotProt 2.0: K
sequence length	125
structure length	124
Chain Sequence	TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

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/5cfd3bdf712f60aed1d2e8ac/pdb.gz): 3501 ms

reading 124 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

124 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:123});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	Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry. pubmed doi rcsb
molecule keywords	AMICYANIN
molecule tags	Oxidoreductase
total genus	31
structure length	124
sequence length	125
chains with identical sequence	M
other databases	KnotProt 2.0: K
ec nomenclature	ec 1.4.9.1: Methylamine dehydrogenase (amicyanin).
pdb deposition date	2006-09-12

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
L	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	2j56L00

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

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

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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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2J56L

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations