2LKM | Genus

Total Genus 46

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	46
sequence length	172
structure length	172
Chain Sequence	SNAEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYRKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV

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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Viewer cachePut cache://localLOAD_/file/5cfd4fdb81a2fe2a04b244dd/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfd4fdb81a2fe2a04b244dd/pdb.gz): 1637 ms

reading 172 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

172 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:171});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	Transcription
source organism	Homo sapiens
publication title	Structural basis for molecular interactions involving MRG domains: implications in chromatin biology. pubmed doi rcsb
molecule keywords	PHD finger protein 12
total genus	46
structure length	172
sequence length	172
ec nomenclature
pdb deposition date	2011-10-16

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.274.30	Mainly Alpha	Orthogonal Bundle	Enzyme I; Chain A, domain 2	Enzyme I; Chain A, domain 2	2lkmB00

2LKMB 2N1DB 2AQLA 2Y0NA 2F5JA
chains in the Genus database with same CATH superfamily

2N3EA 1TWCA 2MX9A 3H0GA 1IW7D 2R7ZA 1W27A 4BABA 3NZ4A 1YNJD 4C5UA 3EZAA 2BE5D 2FIOA 2E2HA 1K83A 2MP0A 4CEHA 2JA5A 2X0QA 2AQLA 4BAAA 1T6PA 1YNND 3EZBA 2K3OA 4CQ5A 2B63A 4CEIA 3GTMA 4C2MA 2FIPA 4CEJA 1Y1WA 2E2IA 4C6GA 2K3NA 5IZ2A 2MQAA 2LKMB 2VK9A 1ZYRD 2N1DB 2JA6A 2YU9A 3CQZA 4FBSA 3GTJA 2R93A 2X0OA 3U4QA 1R9TA 2HROA 1I3QA 3GTKA 2Y0NA 3GTGA 2K3QA 1TWAA 2A6HD 4C5RA 2X0PA 2EZAA 2A68D 3LR8A 2EZBA 2O5JD 3GTLA 2F5JA 1TWFA 3GTQA 2NVXA 2NVYA 3FKIA 2R92A 2A6ED 2LYIA 2EZCA 1WCMA 1TWGA 2HWGA 2JA7A 3GTOA 2MX8A 1I50A 4C5SA 1EZBA 1I6VD 3LRDA 4QIWA 4V2RA 1Y1VA 3LR2A 3GTPA 3EZEA 2LPIA 3LR6A 1TWHA 1T6JA 2LPJA 1EZAA 3U44A 2A69D 4V2QA 1SMYD 1HQMD 1ZYMA 2YIIA 2LTHA 1Y2MA 1SFOA 2VUMA 2CW0D
chains in the Genus database with same CATH topology

2N3EA 1TWCA 2MX9A 3H0GA 1IW7D 2R7ZA 1YNJD 2BE5D 2FIOA 2E2HA 1K83A 4CEHA 2JA5A 2X0QA 2AQLA 1YNND 2K3OA 2B63A 4CEIA 3GTMA 4C2MA 2FIPA 4CEJA 1Y1WA 2E2IA 2K3NA 5IZ2A 2MQAA 2LKMB 2VK9A 1ZYRD 2N1DB 2JA6A 2YU9A 3CQZA 4FBSA 3GTJA 2R93A 2X0OA 3U4QA 1R9TA 1I3QA 3GTKA 2Y0NA 3GTGA 2K3QA 1TWAA 2A6HD 2X0PA 2A68D 3LR8A 2O5JD 3GTLA 2F5JA 1TWFA 3GTQA 2NVXA 2NVYA 3FKIA 2R92A 2A6ED 2LYIA 1WCMA 1TWGA 2JA7A 3GTOA 2MX8A 1I50A 1I6VD 3LRDA 4QIWA 1Y1VA 3LR2A 3GTPA 2LPIA 3LR6A 1TWHA 2LPJA 3U44A 2A69D 1HQMD 1SMYD 2LTHA 2VUMA 1SFOA 2CW0D
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2LKM B;  2N1D B;  2AQL A;  2Y0N A;  2F5J A; 
#chains in the Genus database with same CATH topology
 2N3E A;  1TWC A;  2MX9 A;  3H0G A;  1IW7 D;  2R7Z A;  1W27 A;  4BAB A;  3NZ4 A;  1YNJ D;  4C5U A;  3EZA A;  2BE5 D;  2FIO A;  2E2H A;  1K83 A;  2MP0 A;  4CEH A;  2JA5 A;  2X0Q A;  2AQL A;  4BAA A;  1T6P A;  1YNN D;  3EZB A;  2K3O A;  4CQ5 A;  2B63 A;  4CEI A;  3GTM A;  4C2M A;  2FIP A;  4CEJ A;  1Y1W A;  2E2I A;  4C6G A;  2K3N A;  5IZ2 A;  2MQA A;  2LKM B;  2VK9 A;  1ZYR D;  2N1D B;  2JA6 A;  2YU9 A;  3CQZ A;  4FBS A;  3GTJ A;  2R93 A;  2X0O A;  3U4Q A;  1R9T A;  2HRO A;  1I3Q A;  3GTK A;  2Y0N A;  3GTG A;  2K3Q A;  1TWA A;  2A6H D;  4C5R A;  2X0P A;  2EZA A;  2A68 D;  3LR8 A;  2EZB A;  2O5J D;  3GTL A;  2F5J A;  1TWF A;  3GTQ A;  2NVX A;  2NVY A;  3FKI A;  2R92 A;  2A6E D;  2LYI A;  2EZC A;  1WCM A;  1TWG A;  2HWG A;  2JA7 A;  3GTO A;  2MX8 A;  1I50 A;  4C5S A;  1EZB A;  1I6V D;  3LRD A;  4QIW A;  4V2R A;  1Y1V A;  3LR2 A;  3GTP A;  3EZE A;  2LPI A;  3LR6 A;  1TWH A;  1T6J A;  2LPJ A;  1EZA A;  3U44 A;  2A69 D;  4V2Q A;  1SMY D;  1HQM D;  1ZYM A;  2YII A;  2LTH A;  1Y2M A;  1SFO A;  2VUM A;  2CW0 D; 
#chains in the Genus database with same CATH homology
 2N3E A;  1TWC A;  2MX9 A;  3H0G A;  1IW7 D;  2R7Z A;  1YNJ D;  2BE5 D;  2FIO A;  2E2H A;  1K83 A;  4CEH A;  2JA5 A;  2X0Q A;  2AQL A;  1YNN D;  2K3O A;  2B63 A;  4CEI A;  3GTM A;  4C2M A;  2FIP A;  4CEJ A;  1Y1W A;  2E2I A;  2K3N A;  5IZ2 A;  2MQA A;  2LKM B;  2VK9 A;  1ZYR D;  2N1D B;  2JA6 A;  2YU9 A;  3CQZ A;  4FBS A;  3GTJ A;  2R93 A;  2X0O A;  3U4Q A;  1R9T A;  1I3Q A;  3GTK A;  2Y0N A;  3GTG A;  2K3Q A;  1TWA A;  2A6H D;  2X0P A;  2A68 D;  3LR8 A;  2O5J D;  3GTL A;  2F5J A;  1TWF A;  3GTQ A;  2NVX A;  2NVY A;  3FKI A;  2R92 A;  2A6E D;  2LYI A;  1WCM A;  1TWG A;  2JA7 A;  3GTO A;  2MX8 A;  1I50 A;  1I6V D;  3LRD A;  4QIW A;  1Y1V A;  3LR2 A;  3GTP A;  2LPI A;  3LR6 A;  1TWH A;  2LPJ A;  3U44 A;  2A69 D;  1HQM D;  1SMY D;  2LTH A;  2VUM A;  1SFO A;  2CW0 D;

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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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2LKMB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN