3TMDA

Bd1817, a hdg"y"p protein from bdellovibrio bacteriovorus
Total Genus 110
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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
110
sequence length
305
structure length
305
Chain Sequence
DYVSIRVSTLRGDQKIDFNAYVKINDKMILYLRRGDSFEGERLKRLKDKKLRKMYILTDEENSYRTYLQKNIETAYDDTTGKDIQTRADIIQGSQQNNAEEVFENPENVESYNYCKDAAGKYVNFIMSNAQALSAVMNIENTDKTISHHGVTVSTLSIALAQKLGITDPKKTQLLTLGALLHDYGHHHSPLNLNQPLDSMSPEDLALWKKHPIEGAQKVQDKKHFDQTVINIIGQHEETINGTGPKGLREKDMDPLAVLVSSANAMDRLITFEGVPKAEAAKKLMIDHVGKHPLQHIQHLNDILK
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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 Hydrolase,signaling protein
molecule keywords Uncharacterized protein
publication title The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases.
pubmed doi rcsb
source organism Bdellovibrio bacteriovorus
total genus 110
structure length 305
sequence length 305
ec nomenclature
pdb deposition date 2011-08-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF13487 HD_5 HD domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.3210.10 Mainly Alpha Orthogonal Bundle Hypothetical protein af1432 Hypothetical protein af1432 3tmdA00
4TO1A 4RXOA 4ZWGA 4QG2A 3NQWA 4BZBA 3MZOA 4TNRA 5TKAA 2PARA 2PQ7A 4TNXA 5AO0A 3HC1A 2O08A 3P3QA 4MZ7A 3LJXA 5TK6A 2DQBA 4RXQA 4MLMA 5AO4A 4TNYA 5TK7A 4RXRA 1VJ7A 5TK8A 4QFZA 4TO0A 2FLOA 3BG2A 4ZWEA 3M1TA 4QG1A 4L1JA 3IRHA 3MEMA 4L1JB 4X9EA 4L7WA 3CCGA 4LRLA 4TO5A 3HI0A 4N71A 4QFYA 4TO4A 2PAUA 5AO1A 1YOYA 2GZ4A 2O6IA 4TO6A 3TMBA 5AO2A 4TNPA 2OGIA 5TK9A 3RF0A 3TMDA 1U6ZA 2CQZA 2PGSA 3KH1A 4TNQA 3U1NA 2PAQA 4RXSA 4MCWA 4R8ZA 4TO2A 4QFXA 3TM8A 4L7EA 4QG0A 4QG4A 4N6WA 4Q7HA 4DMBA 1VQRA 1YNBA 4TNZA 2HEKA 3I7AA 1XX7A 2Q14A 4MLNA 4MDZA 4XDSA 4ME4A 3TMCA 5AO3A 4TO3A 3NR1A 4RXPA 4BZCA
chains in the Genus database with same CATH superfamily
4TO1A 4RXOA 4ZWGA 4QG2A 3NQWA 4BZBA 3MZOA 4TNRA 5TKAA 3SK9A 2PARA 2PQ7A 4TNXA 5AO0A 3HC1A 2O08A 3P3QA 4MZ7A 3LJXA 5TK6A 2DQBA 4RXQA 4MLMA 3KQ5A 5AO4A 4TNYA 5TK7A 4RXRA 1VJ7A 5TK8A 4QFZA 4TO0A 2FLOA 3BG2A 4ZWEA 3M1TA 4QG1A 4L1JA 3IRHA 3MEMA 3S4LA 4L1JB 4X9EA 4L7WA 3CCGA 4LRLA 4TO5A 3HI0A 4N71A 4QFYA 4TO4A 2PAUA 5AO1A 1YOYA 2GZ4A 2O6IA 4TO6A 3TMBA 5AO2A 4TNPA 4QQXA 2OGIA 4Q2CA 5TK9A 3RF0A 3TMDA 1U6ZA 2CQZA 2PGSA 3KH1A 4TNQA 3U1NA 2PAQA 4RXSA 4QQZA 4MCWA 4R8ZA 4TO2A 4QFXA 3TM8A 4L7EA 4QG0A 4QQWA 4QG4A 4N6WA 4Q7HA 4DMBA 1VQRA 1YNBA 4TNZA 2HEKA 3I7AA 4Q2DA 1XX7A 2Q14A 4MLNA 4MDZA 4XDSA 4ME4A 4QQYA 3TMCA 5AO3A 4TO3A 3SKDA 3GW7A 3NR1A 4RXPA 4BZCA
chains in the Genus database with same CATH topology
4TO1A 4RXOA 4ZWGA 4QG2A 3NQWA 4BZBA 3MZOA 4TNRA 5TKAA 3SK9A 2PARA 2PQ7A 4TNXA 5AO0A 3HC1A 2O08A 3P3QA 4MZ7A 3LJXA 5TK6A 2DQBA 4RXQA 4MLMA 3KQ5A 5AO4A 4TNYA 5TK7A 4RXRA 1VJ7A 5TK8A 4QFZA 4TO0A 2FLOA 3BG2A 4ZWEA 3M1TA 4QG1A 4L1JA 3IRHA 3MEMA 3S4LA 4L1JB 4X9EA 4L7WA 3CCGA 4LRLA 4TO5A 3HI0A 4N71A 4QFYA 4TO4A 2PAUA 5AO1A 1YOYA 2GZ4A 2O6IA 4TO6A 3TMBA 5AO2A 4TNPA 4QQXA 2OGIA 4Q2CA 5TK9A 3RF0A 3TMDA 1U6ZA 2CQZA 2PGSA 3KH1A 4TNQA 3U1NA 2PAQA 4RXSA 4QQZA 4MCWA 4R8ZA 4TO2A 4QFXA 3TM8A 4L7EA 4QG0A 4QQWA 4QG4A 4N6WA 4Q7HA 4DMBA 1VQRA 1YNBA 4TNZA 2HEKA 3I7AA 4Q2DA 1XX7A 2Q14A 4MLNA 4MDZA 4XDSA 4ME4A 4QQYA 3TMCA 5AO3A 4TO3A 3SKDA 3GW7A 3NR1A 4RXPA 4BZCA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4TO1 A;  4RXO A;  4ZWG A;  4QG2 A;  3NQW A;  4BZB A;  3MZO A;  4TNR A;  5TKA A;  2PAR A;  2PQ7 A;  4TNX A;  5AO0 A;  3HC1 A;  2O08 A;  3P3Q A;  4MZ7 A;  3LJX A;  5TK6 A;  2DQB A;  4RXQ A;  4MLM A;  5AO4 A;  4TNY A;  5TK7 A;  4RXR A;  1VJ7 A;  5TK8 A;  4QFZ A;  4TO0 A;  2FLO A;  3BG2 A;  4ZWE A;  3M1T A;  4QG1 A;  4L1J A;  3IRH A;  3MEM A;  4L1J B;  4X9E A;  4L7W A;  3CCG A;  4LRL A;  4TO5 A;  3HI0 A;  4N71 A;  4QFY A;  4TO4 A;  2PAU A;  5AO1 A;  1YOY A;  2GZ4 A;  2O6I A;  4TO6 A;  3TMB A;  5AO2 A;  4TNP A;  2OGI A;  5TK9 A;  3RF0 A;  3TMD A;  1U6Z A;  2CQZ A;  2PGS A;  3KH1 A;  4TNQ A;  3U1N A;  2PAQ A;  4RXS A;  4MCW A;  4R8Z A;  4TO2 A;  4QFX A;  3TM8 A;  4L7E A;  4QG0 A;  4QG4 A;  4N6W A;  4Q7H A;  4DMB A;  1VQR A;  1YNB A;  4TNZ A;  2HEK A;  3I7A A;  1XX7 A;  2Q14 A;  4MLN A;  4MDZ A;  4XDS A;  4ME4 A;  3TMC A;  5AO3 A;  4TO3 A;  3NR1 A;  4RXP A;  4BZC A; 
#chains in the Genus database with same CATH topology
 4TO1 A;  4RXO A;  4ZWG A;  4QG2 A;  3NQW A;  4BZB A;  3MZO A;  4TNR A;  5TKA A;  3SK9 A;  2PAR A;  2PQ7 A;  4TNX A;  5AO0 A;  3HC1 A;  2O08 A;  3P3Q A;  4MZ7 A;  3LJX A;  5TK6 A;  2DQB A;  4RXQ A;  4MLM A;  3KQ5 A;  5AO4 A;  4TNY A;  5TK7 A;  4RXR A;  1VJ7 A;  5TK8 A;  4QFZ A;  4TO0 A;  2FLO A;  3BG2 A;  4ZWE A;  3M1T A;  4QG1 A;  4L1J A;  3IRH A;  3MEM A;  3S4L A;  4L1J B;  4X9E A;  4L7W A;  3CCG A;  4LRL A;  4TO5 A;  3HI0 A;  4N71 A;  4QFY A;  4TO4 A;  2PAU A;  5AO1 A;  1YOY A;  2GZ4 A;  2O6I A;  4TO6 A;  3TMB A;  5AO2 A;  4TNP A;  4QQX A;  2OGI A;  4Q2C A;  5TK9 A;  3RF0 A;  3TMD A;  1U6Z A;  2CQZ A;  2PGS A;  3KH1 A;  4TNQ A;  3U1N A;  2PAQ A;  4RXS A;  4QQZ A;  4MCW A;  4R8Z A;  4TO2 A;  4QFX A;  3TM8 A;  4L7E A;  4QG0 A;  4QQW A;  4QG4 A;  4N6W A;  4Q7H A;  4DMB A;  1VQR A;  1YNB A;  4TNZ A;  2HEK A;  3I7A A;  4Q2D A;  1XX7 A;  2Q14 A;  4MLN A;  4MDZ A;  4XDS A;  4ME4 A;  4QQY A;  3TMC A;  5AO3 A;  4TO3 A;  3SKD A;  3GW7 A;  3NR1 A;  4RXP A;  4BZC A; 
#chains in the Genus database with same CATH homology
 4TO1 A;  4RXO A;  4ZWG A;  4QG2 A;  3NQW A;  4BZB A;  3MZO A;  4TNR A;  5TKA A;  3SK9 A;  2PAR A;  2PQ7 A;  4TNX A;  5AO0 A;  3HC1 A;  2O08 A;  3P3Q A;  4MZ7 A;  3LJX A;  5TK6 A;  2DQB A;  4RXQ A;  4MLM A;  3KQ5 A;  5AO4 A;  4TNY A;  5TK7 A;  4RXR A;  1VJ7 A;  5TK8 A;  4QFZ A;  4TO0 A;  2FLO A;  3BG2 A;  4ZWE A;  3M1T A;  4QG1 A;  4L1J A;  3IRH A;  3MEM A;  3S4L A;  4L1J B;  4X9E A;  4L7W A;  3CCG A;  4LRL A;  4TO5 A;  3HI0 A;  4N71 A;  4QFY A;  4TO4 A;  2PAU A;  5AO1 A;  1YOY A;  2GZ4 A;  2O6I A;  4TO6 A;  3TMB A;  5AO2 A;  4TNP A;  4QQX A;  2OGI A;  4Q2C A;  5TK9 A;  3RF0 A;  3TMD A;  1U6Z A;  2CQZ A;  2PGS A;  3KH1 A;  4TNQ A;  3U1N A;  2PAQ A;  4RXS A;  4QQZ A;  4MCW A;  4R8Z A;  4TO2 A;  4QFX A;  3TM8 A;  4L7E A;  4QG0 A;  4QQW A;  4QG4 A;  4N6W A;  4Q7H A;  4DMB A;  1VQR A;  1YNB A;  4TNZ A;  2HEK A;  3I7A A;  4Q2D A;  1XX7 A;  2Q14 A;  4MLN A;  4MDZ A;  4XDS A;  4ME4 A;  4QQY A;  3TMC A;  5AO3 A;  4TO3 A;  3SKD A;  3GW7 A;  3NR1 A;  4RXP A;  4BZC 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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