1NVP | Genus

Total Genus 45

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	45
sequence length	180
structure length	180
Chain Sequence	SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKT

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/5d21e9b2000583cabdb27719/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d21e9b2000583cabdb27719/pdb.gz): 1876 ms

reading 180 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

180 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:179});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/dna
source organism	Homo sapiens
publication title	Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. pubmed doi rcsb
molecule keywords	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGP*G)-3'
total genus	45
structure length	180
sequence length	180
ec nomenclature
pdb deposition date	2003-02-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00352	TBP	Transcription factor TFIID (or TATA-binding protein, TBP)

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	1nvpA01
3.30.310.10	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	TATA-Binding Protein	1nvpA02

2IV8A 1RM1A 1KYUA 1D3UA 1PCZA 4ROCB 5IYCP 1QNEA 1QN7A 1QTSA 3HS9A 1QN8A 1W80A 3VN5A 1MP9A 1KY7A 1C9BB 1YTBA 1QN9A 1KYFA 1QTPA 4PY5A 3ASMA 3H1ZA 1QN5A 1TGHA 4WZSD 1E42A 1TBAB 2D0BA 1QN6A 1VTLE 3OCIA 1YTFA 5IYBP 3EIKA 2IV9A 1NH2A 1QN4A 1R4XA 1KY6A 1VTOA 1JFIC 1VOLB 1QNCA 2Z8UA 4RODB 4ROEB 3OC3C 2MJ7A 1AISA 1PZDA 5IYDP 1QN3A 3HS8A 1NGMA 1B9KA 2G30A 1QNAA 1QNBA 4B0AA 1CDWA 1NVPA 2D0CA 1TBPA 1VOKA 2D0AA 1KYDA 2VJ0A
chains in the Genus database with same CATH superfamily

1RM1A 3ENCA 1YQLA 3N89A 1C4GA 2NOHA 1QN7A 3HS9A 2LAEA 1KO9A 3OLPA 1M5Q1 1PCMX 3F10A 2MZ8A 1QTPA 3ASMA 3CWTA 2HL8A 2DKCA 1K2YX 2D0BA 4C7PA 4CFFA 4D7QA 1P5DX 4EALA 3CWUA 1VTLE 1M3HA 1QN6A 4QG5A 4HJHA 1R4XA 1V5SA 1JFIC 1QNCA 2NLVA 2Z8UA 3TDHA 5JMVD 2PWWA 3D7QA 2DKDA 3CVSA 1NGMA 2JPIA 2FGTA 1DIZA 4B0AA 1NVPA 5EPCA 1AISA 1WJWA 2R5XA 2VJ0A 1QNBA 4ROCB 2JHJA 2NOIA 1QNEA 5KL0A 1QTSA 1YQMA 1C47A 1K35A 1TUOA 5F9CA 1W80A 3VN5A 1YQRA 2NOEA 1C9BB 5HSHA 2O3OA 4PY5A 2FUVA 3F0ZA 4BJUA 3T4NA 1XSZA 3OGDA 1TBAB 4D7RA 4EAIA 2V9JA 5AN4A 5IYBP 4EJZA 3ULXA 4EAJA 1VOLB 1M3QA 2F7LA 4ROEB 3OSTA 2QLVA 4RODB 4EAKA 5BMNA 1N3AA 2MJ7A 2NOLA 2NWVA 1QNAA 2JHNA 3ENOC 1JDYA 2Y8LA 2D0CA 1TBPA 2IV8A 2HZSA 2H4LX 3CWAA 1CDWA 5IYDP 1D3UA 4IL8A 1KYUA 1N3CA 1UT7A 2EHBD 5IYCP 3DPTA 3CW7A 3EAYA 2NOBA 2HZMA 3DPUA 1MPGA 1MP9A 1KY7A 3IH7A 1P5GX 2V92A 1HU0A 2HL9A 1N39A 1QN5A 4WZSD 3I0XA 3OSEA 2Y8QA 3UW2A 3C04A 3KTUA 3CVTA 1NH2A 1VKLA 1YQKA 1EBMA 3PMGA 1KY6A 1LWVA 1VTOA 1EUVA 1QN4A 2FKFA 2H5AX 3RSMA 1KFIA 2FKMX 2NOFA 2OOYA 2Z0FA 1B9KA 2NVMA 5BMPA 1WQAA 3I0WA 1FN7A 1KYDA 2YH5A 2OOXA 3BKQX 4MRQA 1PCZA 1UT4A 2I5WA 4WXAA 4WX8A 1QN8A 3PDKA 2QR1A 1T6AA 2V8QA 3OH9A 1LWYA 1YTBA 2NOZA 1QN9A 1PVSA 2YA3A 1KYFA 4TPSA 3H1ZA 1PCJX 2HKPA 2XHIA 1TGHA 3TE5A 1E42A 1LWWA 1Q9UA 3NA5A 5JN5A 3OH6A 3D4VA 2JOIA 1UL7A 2DKAA 2ZFDB 3OCIA 3OSMA 4DULA 1YTFA 3EIKA 2IV9A 3I3WA 4I8OA 1KFQA 2QREA 3CWSA 4Q11A 3SNSA 3OC3C 3KRMA 1PZDA 4EAGA 1QN3A 3HS8A 1J3MA 3RPJA 2G30A 2QRCA 1VOKA 1LXTA 2QRDA 4EJYA 2D0AA
chains in the Genus database with same CATH topology

1RM1A 1YQLA 3N89A 2NOHA 1QN7A 3HS9A 2LAEA 1KO9A 3F10A 2MZ8A 1QTPA 3ASMA 2D0BA 1QN6A 1VTLE 1M3HA 1R4XA 1JFIC 1QNCA 2Z8UA 1NGMA 2FGTA 4B0AA 1NVPA 1AISA 2VJ0A 1QNBA 4ROCB 2NOIA 1QNEA 1QTSA 1YQMA 2NOEA 1W80A 3VN5A 1YQRA 1C9BB 2O3OA 4PY5A 3F0ZA 1TBAB 5AN4A 5IYBP 4EJZA 3ULXA 1VOLB 1M3QA 4ROEB 3OSTA 4RODB 1N3AA 2MJ7A 2NOLA 1QNAA 2D0CA 1TBPA 2IV8A 2HZSA 1CDWA 5IYDP 1D3UA 1KYUA 1N3CA 1UT7A 5IYCP 3DPTA 2NOBA 2HZMA 3DPUA 1MP9A 1KY7A 3IH7A 1HU0A 1N39A 1QN5A 4WZSD 3I0XA 3KTUA 1NH2A 1YQKA 1EBMA 1QN4A 1KY6A 1LWVA 1VTOA 2NOFA 1B9KA 3I0WA 1FN7A 1KYDA 2YH5A 1PCZA 1UT4A 2I5WA 1QN8A 1LWYA 1YTBA 2NOZA 1QN9A 4TPSA 1KYFA 3H1ZA 2XHIA 1TGHA 1LWWA 1E42A 2JOIA 3OCIA 3OSMA 1YTFA 4DULA 3EIKA 2IV9A 4I8OA 4Q11A 3SNSA 3OC3C 3KRMA 1PZDA 1QN3A 3HS8A 3RPJA 2G30A 1VOKA 4EJYA 2D0AA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2IV8 A;  1RM1 A;  1KYU A;  1D3U A;  1PCZ A;  4ROC B;  5IYC P;  1QNE A;  1QN7 A;  1QTS A;  3HS9 A;  1QN8 A;  1W80 A;  3VN5 A;  1MP9 A;  1KY7 A;  1C9B B;  1YTB A;  1QN9 A;  1KYF A;  1QTP A;  4PY5 A;  3ASM A;  3H1Z A;  1QN5 A;  1TGH A;  4WZS D;  1E42 A;  1TBA B;  2D0B A;  1QN6 A;  1VTL E;  3OCI A;  1YTF A;  5IYB P;  3EIK A;  2IV9 A;  1NH2 A;  1QN4 A;  1R4X A;  1KY6 A;  1VTO A;  1JFI C;  1VOL B;  1QNC A;  2Z8U A;  4ROD B;  4ROE B;  3OC3 C;  2MJ7 A;  1AIS A;  1PZD A;  5IYD P;  1QN3 A;  3HS8 A;  1NGM A;  1B9K A;  2G30 A;  1QNA A;  1QNB A;  4B0A A;  1CDW A;  1NVP A;  2D0C A;  1TBP A;  1VOK A;  2D0A A;  1KYD A;  2VJ0 A; 
#chains in the Genus database with same CATH topology
 1RM1 A;  3ENC A;  1YQL A;  3N89 A;  1C4G A;  2NOH A;  1QN7 A;  3HS9 A;  2LAE A;  1KO9 A;  3OLP A;  1M5Q 1;  1PCM X;  3F10 A;  2MZ8 A;  1QTP A;  3ASM A;  3CWT A;  2HL8 A;  2DKC A;  1K2Y X;  2D0B A;  4C7P A;  4CFF A;  4D7Q A;  1P5D X;  4EAL A;  3CWU A;  1VTL E;  1M3H A;  1QN6 A;  4QG5 A;  4HJH A;  1R4X A;  1V5S A;  1JFI C;  1QNC A;  2NLV A;  2Z8U A;  3TDH A;  5JMV D;  2PWW A;  3D7Q A;  2DKD A;  3CVS A;  1NGM A;  2JPI A;  2FGT A;  1DIZ A;  4B0A A;  1NVP A;  5EPC A;  1AIS A;  1WJW A;  2R5X A;  2VJ0 A;  1QNB A;  4ROC B;  2JHJ A;  2NOI A;  1QNE A;  5KL0 A;  1QTS A;  1YQM A;  1C47 A;  1K35 A;  1TUO A;  5F9C A;  1W80 A;  3VN5 A;  1YQR A;  2NOE A;  1C9B B;  5HSH A;  2O3O A;  4PY5 A;  2FUV A;  3F0Z A;  4BJU A;  3T4N A;  1XSZ A;  3OGD A;  1TBA B;  4D7R A;  4EAI A;  2V9J A;  5AN4 A;  5IYB P;  4EJZ A;  3ULX A;  4EAJ A;  1VOL B;  1M3Q A;  2F7L A;  4ROE B;  3OST A;  2QLV A;  4ROD B;  4EAK A;  5BMN A;  1N3A A;  2MJ7 A;  2NOL A;  2NWV A;  1QNA A;  2JHN A;  3ENO C;  1JDY A;  2Y8L A;  2D0C A;  1TBP A;  2IV8 A;  2HZS A;  2H4L X;  3CWA A;  1CDW A;  5IYD P;  1D3U A;  4IL8 A;  1KYU A;  1N3C A;  1UT7 A;  2EHB D;  5IYC P;  3DPT A;  3CW7 A;  3EAY A;  2NOB A;  2HZM A;  3DPU A;  1MPG A;  1MP9 A;  1KY7 A;  3IH7 A;  1P5G X;  2V92 A;  1HU0 A;  2HL9 A;  1N39 A;  1QN5 A;  4WZS D;  3I0X A;  3OSE A;  2Y8Q A;  3UW2 A;  3C04 A;  3KTU A;  3CVT A;  1NH2 A;  1VKL A;  1YQK A;  1EBM A;  3PMG A;  1KY6 A;  1LWV A;  1VTO A;  1EUV A;  1QN4 A;  2FKF A;  2H5A X;  3RSM A;  1KFI A;  2FKM X;  2NOF A;  2OOY A;  2Z0F A;  1B9K A;  2NVM A;  5BMP A;  1WQA A;  3I0W A;  1FN7 A;  1KYD A;  2YH5 A;  2OOX A;  3BKQ X;  4MRQ A;  1PCZ A;  1UT4 A;  2I5W A;  4WXA A;  4WX8 A;  1QN8 A;  3PDK A;  2QR1 A;  1T6A A;  2V8Q A;  3OH9 A;  1LWY A;  1YTB A;  2NOZ A;  1QN9 A;  1PVS A;  2YA3 A;  1KYF A;  4TPS A;  3H1Z A;  1PCJ X;  2HKP A;  2XHI A;  1TGH A;  3TE5 A;  1E42 A;  1LWW A;  1Q9U A;  3NA5 A;  5JN5 A;  3OH6 A;  3D4V A;  2JOI A;  1UL7 A;  2DKA A;  2ZFD B;  3OCI A;  3OSM A;  4DUL A;  1YTF A;  3EIK A;  2IV9 A;  3I3W A;  4I8O A;  1KFQ A;  2QRE A;  3CWS A;  4Q11 A;  3SNS A;  3OC3 C;  3KRM A;  1PZD A;  4EAG A;  1QN3 A;  3HS8 A;  1J3M A;  3RPJ A;  2G30 A;  2QRC A;  1VOK A;  1LXT A;  2QRD A;  4EJY A;  2D0A A; 
#chains in the Genus database with same CATH homology
 1RM1 A;  1YQL A;  3N89 A;  2NOH A;  1QN7 A;  3HS9 A;  2LAE A;  1KO9 A;  3F10 A;  2MZ8 A;  1QTP A;  3ASM A;  2D0B A;  1QN6 A;  1VTL E;  1M3H A;  1R4X A;  1JFI C;  1QNC A;  2Z8U A;  1NGM A;  2FGT A;  4B0A A;  1NVP A;  1AIS A;  2VJ0 A;  1QNB A;  4ROC B;  2NOI A;  1QNE A;  1QTS A;  1YQM A;  2NOE A;  1W80 A;  3VN5 A;  1YQR A;  1C9B B;  2O3O A;  4PY5 A;  3F0Z A;  1TBA B;  5AN4 A;  5IYB P;  4EJZ A;  3ULX A;  1VOL B;  1M3Q A;  4ROE B;  3OST A;  4ROD B;  1N3A A;  2MJ7 A;  2NOL A;  1QNA A;  2D0C A;  1TBP A;  2IV8 A;  2HZS A;  1CDW A;  5IYD P;  1D3U A;  1KYU A;  1N3C A;  1UT7 A;  5IYC P;  3DPT A;  2NOB A;  2HZM A;  3DPU A;  1MP9 A;  1KY7 A;  3IH7 A;  1HU0 A;  1N39 A;  1QN5 A;  4WZS D;  3I0X A;  3KTU A;  1NH2 A;  1YQK A;  1EBM A;  1QN4 A;  1KY6 A;  1LWV A;  1VTO A;  2NOF A;  1B9K A;  3I0W A;  1FN7 A;  1KYD A;  2YH5 A;  1PCZ A;  1UT4 A;  2I5W A;  1QN8 A;  1LWY A;  1YTB A;  2NOZ A;  1QN9 A;  4TPS A;  1KYF A;  3H1Z A;  2XHI A;  1TGH A;  1LWW A;  1E42 A;  2JOI A;  3OCI A;  3OSM A;  1YTF A;  4DUL A;  3EIK A;  2IV9 A;  4I8O A;  4Q11 A;  3SNS A;  3OC3 C;  3KRM A;  1PZD A;  1QN3 A;  3HS8 A;  3RPJ A;  2G30 A;  1VOK A;  4EJY A;  2D0A 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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1NVPA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations