4BPX | Genus

Total Genus 50

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	50
sequence length	217
structure length	181
Chain Sequence	ISLIEFENLAIDRVKLLKSVENLSKLESELRKLRRDHISHFILRLAYCQSEELRRWFIQQEMDLLRFRFSILPKDKIQDFLKDSQLQFEAISDEEKTLREQEIVASSPSLLGFESIYKIPFADALDLFRGRKVYLEDGFAYVPLKDIVAIILNEFRAKLSKALALTARSLDERLQPLLNHL

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/5d0392399124529dc5a25092/pdb.gz): 1794 ms

reading 181 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

181 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:180});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	Transferase
source organism	Homo sapiens
publication title	Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering pubmed doi rcsb
molecule keywords	DNA PRIMASE SMALL SUBUNIT
total genus	50
structure length	181
sequence length	217
chains with identical sequence	D
ec nomenclature	ec 2.7.7.-:
pdb deposition date	2013-05-28

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.930.80	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II; Chain A	Transcription Elongation Factor S-II; Chain A	4bpxB00

4BPXB 4BPUB 4BPWB 4RR2B
chains in the Genus database with same CATH superfamily

2CBLA 4OC0A 1Z9EA 3BXMA 4MCRA 3FEDA 4P4IA 4OMEA 3D7FA 4NGTA 3PLFB 3VRNA 3S9NA 5F13A 1WJTA 3S9LA 4MCSA 2PVWA 4P4EA 5F09A 2XPLA 1DE4C 3D7DA 3U88C 2OOTA 4BTFA 4NGRA 1B47A 3VRQA 4X3RA 3PFVA 1YVHA 1Z8LA 3BHXA 4MCPA 2C6CA 4OC1A 5D29A 3F9KC 3HPHE 2XPOA 3OB2B 2JBJA 4NGQA 3ZNIA 3BUMB 3VROA 4A4CA 3BI1A 3D7GA 4P45A 3HPGG 4OC3A 2C6PA 4P4DA 3KASA 3IWWA 3NFQA 4P44A 2XEJA 3OAKA 2B4JC 3FEEA 2C6GA 2JBKA 2N3AB 5HKZA 4A4BA 4NGMA 4BPUB 1FBVA 1EO0A 3S9MA 2DLAA 3BUNB 3OP0A 3HMJG 3RBUA 4W9YA 2XEGA 2PVVA 2VKZG 3FECA 4BPXB 4JZ0A 4BPWB 4NGNA 4NGPA 4RR2B 3O8ZA 4OC5A 2XPNA 1CX8A 3VGOA 4P4BA 2CIJA 2Y1MA 3PT1A 4OC4A 4OC2A 3BI0A 2XEFA 2XEIA 4LQGA 5J3XA 4MCQA 5BY0A 2OR4A 4P4FA 5AXIA 3VRRA 2UV8G 5HKYA 3BUOB 3SJEA 3SJGA 3BUWB 4P4JA 3SJXA 4JYWA 3BUXB 2Y1NA 3SJFA 3OB1B 4GPLB 4NGSA 2XPPA 3FF3A 3VRPA 5ELYA 3D7HA 5HKWA
chains in the Genus database with same CATH topology

4BPXB 2DLAA 2UV8G 3HMJG 4BPWB 5F13A 4BPUB 3PT1A 5BY0A 4RR2B 2VKZG
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4BPX B;  4BPU B;  4BPW B;  4RR2 B; 
#chains in the Genus database with same CATH topology
 2CBL A;  4OC0 A;  1Z9E A;  3BXM A;  4MCR A;  3FED A;  4P4I A;  4OME A;  3D7F A;  4NGT A;  3PLF B;  3VRN A;  3S9N A;  5F13 A;  1WJT A;  3S9L A;  4MCS A;  2PVW A;  4P4E A;  5F09 A;  2XPL A;  1DE4 C;  3D7D A;  3U88 C;  2OOT A;  4BTF A;  4NGR A;  1B47 A;  3VRQ A;  4X3R A;  3PFV A;  1YVH A;  1Z8L A;  3BHX A;  4MCP A;  2C6C A;  4OC1 A;  5D29 A;  3F9K C;  3HPH E;  2XPO A;  3OB2 B;  2JBJ A;  4NGQ A;  3ZNI A;  3BUM B;  3VRO A;  4A4C A;  3BI1 A;  3D7G A;  4P45 A;  3HPG G;  4OC3 A;  2C6P A;  4P4D A;  3KAS A;  3IWW A;  3NFQ A;  4P44 A;  2XEJ A;  3OAK A;  2B4J C;  3FEE A;  2C6G A;  2JBK A;  2N3A B;  5HKZ A;  4A4B A;  4NGM A;  4BPU B;  1FBV A;  1EO0 A;  3S9M A;  2DLA A;  3BUN B;  3OP0 A;  3HMJ G;  3RBU A;  4W9Y A;  2XEG A;  2PVV A;  2VKZ G;  3FEC A;  4BPX B;  4JZ0 A;  4BPW B;  4NGN A;  4NGP A;  4RR2 B;  3O8Z A;  4OC5 A;  2XPN A;  1CX8 A;  3VGO A;  4P4B A;  2CIJ A;  2Y1M A;  3PT1 A;  4OC4 A;  4OC2 A;  3BI0 A;  2XEF A;  2XEI A;  4LQG A;  5J3X A;  4MCQ A;  5BY0 A;  2OR4 A;  4P4F A;  5AXI A;  3VRR A;  2UV8 G;  5HKY A;  3BUO B;  3SJE A;  3SJG A;  3BUW B;  4P4J A;  3SJX A;  4JYW A;  3BUX B;  2Y1N A;  3SJF A;  3OB1 B;  4GPL B;  4NGS A;  2XPP A;  3FF3 A;  3VRP A;  5ELY A;  3D7H A;  5HKW A; 
#chains in the Genus database with same CATH homology
 4BPX B;  2DLA A;  2UV8 G;  3HMJ G;  4BPW B;  5F13 A;  4BPU B;  3PT1 A;  5BY0 A;  4RR2 B;  2VKZ G;

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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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4BPXB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN