1KB4 | Genus

Total Genus 24

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	24
sequence length	93
structure length	93
Chain Sequence	RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEE

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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reading 93 atoms

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1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

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93 atoms created

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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	Structural basis of VDR-DNA interactions on direct repeat response elements. pubmed doi rcsb
molecule keywords	5'-D(CPAPCPAPGPGPTPCPAPCPGPAPAPGPGPTPCPA)-
total genus	24
structure length	93
sequence length	93
chains with identical sequence	B
ec nomenclature
pdb deposition date	2001-11-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00105	zf-C4	Zinc finger, C4 type (two domains)

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1; Chain A	Erythroid Transcription Factor GATA-1, subunit A	1kb4A00

1BY4A 1GLUA 3M9EA 2GDAA 1GATA 1LV3A 2FF0A 1DSZB 1RXRA 4HC9A 4CN5A 1KB6A 5CC1A 3G9IA 2VUUI 5E6CA 5E6DA 5GATA 5E6AA 3G6QA 5L0MA 4TNTA 1GNFA 3G6TA 1R0NA 1DSZA 3G8UA 4GATA 3DFVC 3G6PA 3G6UA 5CBZA 4CN2C 3G6RA 3DZYD 5EMPA 3DZYA 1GA5A 5E6BA 7GATA 3G9MA 4TMAI 1LO1A 2KAEA 4OV7A 3G99A 5EMCA 4ONDA 1LATA 3CBBA 1KB4A 4HCAA 3VEKC 2VUTI 1HRAA 5CBXA 3VD6C 3G8XA 3E00A 1HCPA 2A66A 5KRBB 4OORA 5EMQA 1R4OA 5E69A 1GAUA 2NLLB 4IQRA 3G9PA 1R0OB 3FYLA 3G97A 2C7AA 1KB2A 1CITA 3DFXA 5CC0A 2NLLA 3E00D 1A6YA 3DZUD 3G9JA 5CBYA 4HN5A 3G9OA 1HCQA 3DZUA 1R0OA 2ENVA 1YNWB 4CN3D 4AA6A 1R0NB 1GDCA 4CN3A 4HC7A 2HANB 1R4RA 2VUSI 2EBLA 1RGDA 1R4IA 4CN7A 4NQAB 1YNWA 6GATA 4HN6A 3GATA 1HLZA 2GATA 2HANA 2M9WA 4OLNA
chains in the Genus database with same CATH superfamily

1BY4A 1GLUA 3M9EA 2GDAA 1GATA 1LV3A 2FF0A 1DSZB 1RXRA 4HC9A 4CN5A 1KB6A 5CC1A 3G9IA 2VUUI 5E6CA 5E6DA 5GATA 5E6AA 3G6QA 5L0MA 3G27A 4TNTA 1GNFA 3G6TA 1R0NA 1DSZA 3G8UA 4GATA 2DS8A 3DFVC 3G6PA 3G6UA 5CBZA 4CN2C 3G6RA 3DZYD 5EMPA 3DZYA 1GA5A 5E6BA 7GATA 3G9MA 4TMAI 2DS5A 2KAEA 1LO1A 4OV7A 3G99A 5EMCA 4ONDA 1LATA 3CBBA 1KB4A 4HCAA 3VEKC 2VUTI 1HRAA 5CBXA 3VD6C 3G8XA 3E00A 1HCPA 2A66A 5KRBB 4OORA 5EMQA 1R4OA 5E69A 1GAUA 2NLLB 4IQRA 3G9PA 1R0OB 3FYLA 3G97A 2C7AA 1KB2A 1CITA 3DFXA 5CC0A 2NLLA 3E00D 1A6YA 2DS6A 3DZUD 3G9JA 5CBYA 4HN5A 3G9OA 1HCQA 3DZUA 1R0OA 2ENVA 1YNWB 4CN3D 4AA6A 1R0NB 1GDCA 4CN3A 4HC7A 2HANB 1R4RA 2VUSI 2EBLA 1RGDA 1R4IA 4CN7A 4NQAB 1YNWA 6GATA 4HN6A 3GATA 1HLZA 2GATA 2HANA 2M9WA 4OLNA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1BY4 A;  1GLU A;  3M9E A;  2GDA A;  1GAT A;  1LV3 A;  2FF0 A;  1DSZ B;  1RXR A;  4HC9 A;  4CN5 A;  1KB6 A;  5CC1 A;  3G9I A;  2VUU I;  5E6C A;  5E6D A;  5GAT A;  5E6A A;  3G6Q A;  5L0M A;  4TNT A;  1GNF A;  3G6T A;  1R0N A;  1DSZ A;  3G8U A;  4GAT A;  3DFV C;  3G6P A;  3G6U A;  5CBZ A;  4CN2 C;  3G6R A;  3DZY D;  5EMP A;  3DZY A;  1GA5 A;  5E6B A;  7GAT A;  3G9M A;  4TMA I;  1LO1 A;  2KAE A;  4OV7 A;  3G99 A;  5EMC A;  4OND A;  1LAT A;  3CBB A;  1KB4 A;  4HCA A;  3VEK C;  2VUT I;  1HRA A;  5CBX A;  3VD6 C;  3G8X A;  3E00 A;  1HCP A;  2A66 A;  5KRB B;  4OOR A;  5EMQ A;  1R4O A;  5E69 A;  1GAU A;  2NLL B;  4IQR A;  3G9P A;  1R0O B;  3FYL A;  3G97 A;  2C7A A;  1KB2 A;  1CIT A;  3DFX A;  5CC0 A;  2NLL A;  3E00 D;  1A6Y A;  3DZU D;  3G9J A;  5CBY A;  4HN5 A;  3G9O A;  1HCQ A;  3DZU A;  1R0O A;  2ENV A;  1YNW B;  4CN3 D;  4AA6 A;  1R0N B;  1GDC A;  4CN3 A;  4HC7 A;  2HAN B;  1R4R A;  2VUS I;  2EBL A;  1RGD A;  1R4I A;  4CN7 A;  4NQA B;  1YNW A;  6GAT A;  4HN6 A;  3GAT A;  1HLZ A;  2GAT A;  2HAN A;  2M9W A;  4OLN A; 
#chains in the Genus database with same CATH topology
 1BY4 A;  1GLU A;  3M9E A;  2GDA A;  1GAT A;  1LV3 A;  2FF0 A;  1DSZ B;  1RXR A;  4HC9 A;  4CN5 A;  1KB6 A;  5CC1 A;  3G9I A;  2VUU I;  5E6C A;  5E6D A;  5GAT A;  5E6A A;  3G6Q A;  5L0M A;  3G27 A;  4TNT A;  1GNF A;  3G6T A;  1R0N A;  1DSZ A;  3G8U A;  4GAT A;  2DS8 A;  3DFV C;  3G6P A;  3G6U A;  5CBZ A;  4CN2 C;  3G6R A;  3DZY D;  5EMP A;  3DZY A;  1GA5 A;  5E6B A;  7GAT A;  3G9M A;  4TMA I;  2DS5 A;  2KAE A;  1LO1 A;  4OV7 A;  3G99 A;  5EMC A;  4OND A;  1LAT A;  3CBB A;  1KB4 A;  4HCA A;  3VEK C;  2VUT I;  1HRA A;  5CBX A;  3VD6 C;  3G8X A;  3E00 A;  1HCP A;  2A66 A;  5KRB B;  4OOR A;  5EMQ A;  1R4O A;  5E69 A;  1GAU A;  2NLL B;  4IQR A;  3G9P A;  1R0O B;  3FYL A;  3G97 A;  2C7A A;  1KB2 A;  1CIT A;  3DFX A;  5CC0 A;  2NLL A;  3E00 D;  1A6Y A;  2DS6 A;  3DZU D;  3G9J A;  5CBY A;  4HN5 A;  3G9O A;  1HCQ A;  3DZU A;  1R0O A;  2ENV A;  1YNW B;  4CN3 D;  4AA6 A;  1R0N B;  1GDC A;  4CN3 A;  4HC7 A;  2HAN B;  1R4R A;  2VUS I;  2EBL A;  1RGD A;  1R4I A;  4CN7 A;  4NQA B;  1YNW A;  6GAT A;  4HN6 A;  3GAT A;  1HLZ A;  2GAT A;  2HAN A;  2M9W A;  4OLN A; 
#chains in the Genus database with same CATH homology
 1BY4 A;  1GLU A;  3M9E A;  2GDA A;  1GAT A;  1LV3 A;  2FF0 A;  1DSZ B;  1RXR A;  4HC9 A;  4CN5 A;  1KB6 A;  5CC1 A;  3G9I A;  2VUU I;  5E6C A;  5E6D A;  5GAT A;  5E6A A;  3G6Q A;  5L0M A;  4TNT A;  1GNF A;  3G6T A;  1R0N A;  1DSZ A;  3G8U A;  4GAT A;  3DFV C;  3G6P A;  3G6U A;  5CBZ A;  4CN2 C;  3G6R A;  3DZY D;  5EMP A;  3DZY A;  1GA5 A;  5E6B A;  7GAT A;  3G9M A;  4TMA I;  1LO1 A;  2KAE A;  4OV7 A;  3G99 A;  5EMC A;  4OND A;  1LAT A;  3CBB A;  1KB4 A;  4HCA A;  3VEK C;  2VUT I;  1HRA A;  5CBX A;  3VD6 C;  3G8X A;  3E00 A;  1HCP A;  2A66 A;  5KRB B;  4OOR A;  5EMQ A;  1R4O A;  5E69 A;  1GAU A;  2NLL B;  4IQR A;  3G9P A;  1R0O B;  3FYL A;  3G97 A;  2C7A A;  1KB2 A;  1CIT A;  3DFX A;  5CC0 A;  2NLL A;  3E00 D;  1A6Y A;  3DZU D;  3G9J A;  5CBY A;  4HN5 A;  3G9O A;  1HCQ A;  3DZU A;  1R0O A;  2ENV A;  1YNW B;  4CN3 D;  4AA6 A;  1R0N B;  1GDC A;  4CN3 A;  4HC7 A;  2HAN B;  1R4R A;  2VUS I;  2EBL A;  1RGD A;  1R4I A;  4CN7 A;  4NQA B;  1YNW A;  6GAT A;  4HN6 A;  3GAT A;  1HLZ A;  2GAT A;  2HAN A;  2M9W A;  4OLN A;

1KB4A 1KB6A 1R0NB 1R0OB 1YNWA 2HANB 4IQRA 4UMME 8HBMB
similar chains in the Genus database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the Genus database (40% sequence similarity)
1KB4 A; 1KB6 A; 1R0N B; 1R0O B; 1YNW A; 2HAN B; 4IQR A; 4UMM E; 8HBM B; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)

1KB4A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations