1VTOA

1.9 a resolution refined structure of tbp recognizing the minor groove of tataaaag
Total Genus 45
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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
187
structure length
187
Chain Sequence
VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Transcription/dna
publication title 1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG
pubmed rcsb
molecule keywords DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
total genus 45
structure length 187
sequence length 187
chains with identical sequence B
ec nomenclature
pdb deposition date 1996-09-06

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
ClassArchitectureTopologyHomologyDomain
3.30.310.10 Alpha Beta 2-Layer Sandwich TATA-Binding Protein TATA-Binding Protein 1vtoA01
3.30.310.10 Alpha Beta 2-Layer Sandwich TATA-Binding Protein TATA-Binding Protein 1vtoA02
4PY5A 1CDWA 3EIKA 1KY7A 1W80A 2Z8UA 4ROCB 1E42A 1QN3A 1VOKA 2D0BA 1PZDA 2MJ7A 1QNCA 3HS9A 1QN6A 3HS8A 1NGMA 3ASMA 1YTFA 3VN5A 1QN4A 2G30A 1C9BB 3H1ZA 3OC3C 2D0AA 4RODB 1QN9A 1QNEA 1AISA 1TBPA 1TGHA 1PCZA 1QNAA 2IV9A 4ROEB 4B0AA 3OCIA 1QTPA 1QN7A 2IV8A 1MP9A 1KY6A 1NVPA 1D3UA 1VTOA 1VTLE 1KYUA 5IYBP 1KYDA 1QNBA 1B9KA 1KYFA 1VOLB 5IYCP 5IYDP 1QTSA 4WZSD 2VJ0A 1NH2A 1YTBA 1TBAB 2D0CA 1R4XA 1JFIC 1RM1A 1QN8A 1QN5A
chains in the Genus database with same CATH superfamily
2NOLA 1KY7A 1K35A 2NWVA 2V8QA 1YQLA 1E42A 3OH6A 3EAYA 1QN3A 4QG5A 1XSZA 4Q11A 1M5Q1 3HS8A 4EAKA 1WQAA 1MPGA 3OC3C 4BJUA 4CFFA 5JN5A 1AISA 1QNEA 2DKCA 3DPTA 2FKFA 1JDYA 4EJZA 2HZSA 4ROEB 3OSEA 3I0XA 1QN7A 2NOBA 2V92A 4C7PA 1K2YX 1MP9A 1UL7A 1NVPA 1P5GX 2FUVA 3PDKA 1VTOA 1VTLE 2Z0FA 1QNBA 3PMGA 2JHJA 2QLVA 1NH2A 1YTBA 3T4NA 1N3CA 3CVSA 1M3HA 2NOHA 1JFIC 1CDWA 5AN4A 3I3WA 1Q9UA 3SNSA 1VKLA 3NA5A 3D4VA 1EBMA 2HL9A 2HKPA 2F7LA 2MJ7A 2OOYA 1PZDA 4EJYA 3RSMA 5EPCA 4EAIA 3ASMA 2R5XA 3UW2A 1YTFA 2NOZA 4DULA 1T6AA 4WX8A 3H1ZA 1C9BB 3ENOC 2JHNA 2FGTA 2XHIA 1TBPA 3OH9A 2PWWA 3OSMA 3CWSA 3OSTA 1J3MA 2NLVA 2YH5A 2O3OA 3DPUA 3BKQX 1KYDA 5KL0A 1YQRA 3CWTA 1B9KA 1VOLB 2NOFA 2QREA 5IYCP 1KO9A 1QTSA 4WXAA 2NOIA 1TBAB 2YA3A 2HL8A 1WJWA 1QN8A 1QN5A 2QRCA 3EIKA 1FN7A 3F10A 2JOIA 3TE5A 3RPJA 2Y8QA 1W80A 3C04A 4MRQA 5BMPA 4EALA 3CW7A 1LWYA 5BMNA 1N3AA 3HS9A 4D7RA 1NGMA 2NOEA 3IH7A 1QN4A 2G30A 3KRMA 4RODB 1M3QA 3I0WA 1DIZA 3D7QA 3CWUA 1TGHA 2H5AX 1QNAA 4EAGA 3TDHA 2JPIA 4D7QA 1HU0A 4B0AA 1C47A 1QTPA 1KFQA 3F0ZA 2H4LX 1KY6A 2NVMA 4IL8A 1D3UA 2I5WA 1EUVA 1KYUA 2QR1A 1KFIA 5IYDP 2DKAA 1TUOA 4EAJA 2D0CA 2EHBD 2ZFDB 5JMVD 2FKMX 2MZ8A 3OLPA 2OOXA 1LWVA 4HJHA 3ENCA 1UT7A 3OGDA 2Z8UA 4ROCB 1LWWA 1VOKA 2D0BA 1QN6A 5F9CA 1P5DX 1UT4A 2HZMA 3VN5A 1QNCA 4PY5A 1V5SA 1QN9A 2D0AA 1PCJX 2QRDA 4TPSA 3CWAA 1PCZA 1N39A 2IV9A 2V9JA 1PVSA 3OCIA 5HSHA 3KTUA 1YQKA 2IV8A 3CVTA 1YQMA 1PCMX 1RM1A 3N89A 5IYBP 2Y8LA 4I8OA 1KYFA 3ULXA 4WZSD 2VJ0A 2DKDA 1C4GA 1R4XA 2LAEA 1LXTA
chains in the Genus database with same CATH topology
2NOLA 1KY7A 1YQLA 1E42A 1QN3A 4Q11A 3HS8A 3OC3C 1QNEA 1AISA 3DPTA 4EJZA 2HZSA 4ROEB 3I0XA 1QN7A 2NOBA 1MP9A 1NVPA 1VTOA 1VTLE 1QNBA 1NH2A 1YTBA 2NOHA 1N3CA 1M3HA 1JFIC 1CDWA 5AN4A 3SNSA 1EBMA 2MJ7A 1PZDA 4EJYA 2NOZA 1YTFA 3ASMA 4DULA 1C9BB 3H1ZA 2FGTA 2XHIA 1TBPA 3OSMA 3OSTA 2YH5A 2O3OA 3DPUA 1KYDA 1YQRA 1B9KA 1VOLB 2NOFA 5IYCP 1KO9A 1QTSA 2NOIA 1TBAB 1QN8A 1QN5A 3EIKA 1FN7A 3F10A 2JOIA 3RPJA 1W80A 1LWYA 1N3AA 3HS9A 1NGMA 2NOEA 3IH7A 1QN4A 2G30A 3KRMA 4RODB 1M3QA 3I0WA 1TGHA 2LAEA 1QNAA 1HU0A 4B0AA 1QTPA 3F0ZA 1KY6A 1D3UA 2I5WA 1KYUA 5IYDP 2D0CA 2MZ8A 1LWVA 1UT7A 2Z8UA 4ROCB 1LWWA 1VOKA 2D0BA 1QN6A 1UT4A 2HZMA 3VN5A 1QNCA 4PY5A 1QN9A 2D0AA 4TPSA 1PCZA 1N39A 2IV9A 3OCIA 1YQKA 3KTUA 2IV8A 1YQMA 3N89A 5IYBP 4I8OA 1KYFA 3ULXA 4WZSD 2VJ0A 1R4XA 1RM1A
chains in the Genus database with same CATH homology


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