3EZJA

Crystal structure of the n-terminal domain of the secretin gspd from etec determined with the assistance of a nanobody
Total Genus 58
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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
58
sequence length
233
structure length
198
Chain Sequence
ATFTANFKDTDLKSFIETVGANLNKTIIMVQGAVSIRTMTPLNERQYYQLFLNLLEAQGYAVVPMENDVLKVVKSGDEMVTKVVPVRNVSVRELAPILRQMIDSAGSGNVVNYDPSNVIMLTGRASVVERLTEVIQRVDHAGNRTEEVIPLDNASASEIARVLESLTQIVADERTNSVIVSGDPATRDKMRRLIRRLD
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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 Protein transport
molecule keywords General secretion pathway protein GspD
publication title Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.
pubmed doi rcsb
source organism Escherichia coli
total genus 58
structure length 198
sequence length 233
chains with identical sequence C, E, G
ec nomenclature
pdb deposition date 2008-10-22

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03958 Secretin_N Bacterial type II/III secretion system short domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1370.120 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1 Ribosomal Protein S8; Chain: A, domain 1 3ezjA02
3.30.1370.120 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1 Ribosomal Protein S8; Chain: A, domain 1 3ezjA03
3.55.50.30 Alpha Beta 3-Layer(bab) Sandwich Phage tail protein beta-alpha-beta fold Phage tail protein beta-alpha-beta fold 3ezjA01
2W6TA 2W78A 2W77A 4E9JA 2O5PA 2D1UA 2W6UA 2W16A 4G08A 2A02A 3OSSD 4M0NA 1ZZVA 2IAHA 2W76A 2M5JA 3EZJA 2Y3MA 3GR5A 4JTMA 4EC5A 2W75A 4M0HA 4AR0A
chains in the Genus database with same CATH superfamily
4DR3H 3T1YH 2W78A 1PQXA 2VQEH 1XMOH 3L7ZC 2OPVA 4JI0H 1K28D 2ANRA 2P2RA 2QNDA 4JI7H 1ZZJA 1XNQH 3QD7X 2JEAI 4DR1H 1SEIA 2YQRA 2W16A 5FLXW 1UG8A 2JEBI 1HNXH 4NBQA 1HR0H 4OD6A 1J5EH 2FMRA 4JVHA 4B3TH 4PDBA 2LF0A 4DR7H 4LFBH 2CPQA 2UXDH 4DR4H 1NXUA 4NXNH 2BA0A 1V8CA 3GR5A 2UUCH 3GS9A 1F0XA 2CTLA 4EC5A 4DV0H 4DR5H 3J81W 2CWFA 4LF6H 4KHPH 4M0HA 2FFMA 4LFCH 4AR0A 2LTLA 4MTKA 2NN6G 4DV6H 2AXYA 1ZTGA 5DT9A 4WALA 4X65H 4DV2H 2G8YA 4JI4H 2UXCH 1S20A 2M6QA 2E5LH 4DV3H 4LF5H 3KDGA 3VKEA 1VIGA 2D9IA 2DGRA 2O5PA 2HHHH 1WTJA 5A2QW 4G08A 4FJUA 2A02A 2WZPR 1X4MA 2Z6BD 1EC6A 5K36G 1IBKH 4JYAH 3CDDA 4WANA 3GABA 4M0NA 4UHVA 2ANNA 4B3MH 2PT7G 2JA9A 2CTMA 4NXMH 4JI8H 2UU9H 1X0AA 2LTMA 3EZJA 3J80W 3RF2A 4IFDG 3U1KA 1WTHD 2CTFA 2M8WA 2K1HA 1N36H 1X4NA 4H8AA 1AN7A 4JI5H 1ZZVA 2FPHX 4X62H 1ODHA 4LF8H 1X9ZA 4X64H 4K0KH 4BA2I 2W77A 5IT9W 2ZQEA 4E9JA 3GKUA 4DR6H 1I6UA 1WRUA 2JVZA 4YHHH 5LMUH 1N33H 4B3RH 4DR2H 1Z2IA 3NCVA 3V69A 2ZM6H 1WE8A 2W6UA 1DTJA 2CPMA 1VIHA 1ZZKA 1V9NA 5LMNH 2PQUA 4JI2H 2F4VH 4DV7H 4LF9H 1MSZA 3I0PA 3OV5A 4B8CD 2BL5A 2HH2A 3KDKA 2W76A 2CTEA 4OX9H 2VQFH 1XRHA 4JV5H 1DT4A 4BA1I 3J7AK 1TUAA 4LIJA 2Y3MA 1HNZH 5C0XG 4X66H 4JTMA 4DV4H 4LFAH 1FJGH 2VKCA 3D37A 5JEAG 1KHMA 3FAUA 4YY3H 1VBIA 4NZTM 4JVYA 2W6TA 1XMQH 4DUYH 4LF4H 3JAMW 2A1SA 2CTJA 2MJHA 2CWHA 1I94H 4JI1H 4DUZH 2E3UA 1ZZIA 4AIMA 5LL6b 4JI3H 1XNRH 3AEVB 5IWAH 1WVNA 4DV5H 2UUAH 3T1HH 2UXBH 2UUBH 3ADYA 4GKJH 2D1UA 2OPUA 5BR8H 1N34H 2JZXA 4LF7H 4B3SH 3OSSD 4B8TA 2L4WA 4AM3A 2X06A 2JE6I 1J4WA 4FJSA 1J5KA 1N32H 2PY9A 2Z0SA 4OCHA 3SB1A 4OO1G 2X531 2IAHA 4AQYH 1HNWH 1S03G 1K1GA 2CTKA 4GKKH 2M5JA 2P5ZX 4NZRM 4QMFB 1WHRA 2O4CA 1IBMH 2HH3A 3OTOH 4DV1H 2W75A 3OETA 1FKAH 3UOEA 2LRRA 4JI6H 1IBLH
chains in the Genus database with same CATH topology
4DR3H 3T1YH 2W78A 1XMOH 2VQEH 4JI0H 1K28D 4JI7H 1XNQH 3QD7X 4DR1H 1SEIA 2W16A 5FLXW 1HNXH 1HR0H 4OD6A 1J5EH 4B3TH 4PDBA 2LF0A 4DR7H 4LFBH 2UXDH 4DR4H 4NXNH 3GR5A 2UUCH 3GS9A 1F0XA 4EC5A 4DV0H 4DR5H 4LF6H 3J81W 4KHPH 4M0HA 4LFCH 4AR0A 4DV6H 5DT9A 4DV2H 4X65H 4JI4H 2UXCH 2E5LH 4DV3H 4LF5H 2D9IA 2O5PA 2HHHH 5A2QW 4G08A 2A02A 2WZPR 2Z6BD 1IBKH 4JYAH 3GABA 4M0NA 4B3MH 2PT7G 4NXMH 4JI8H 2UU9H 3EZJA 3J80W 3RF2A 1WTHD 1N36H 1ZZVA 1AN7A 4JI5H 2FPHX 4X62H 1ODHA 4LF8H 1X9ZA 4X64H 4K0KH 2W77A 5IT9W 2ZQEA 4E9JA 4DR6H 1I6UA 4YHHH 5LMUH 1N33H 4B3RH 4DR2H 3NCVA 2ZM6H 2W6UA 5LMNH 4JI2H 2F4VH 4DV7H 4LF9H 3OV5A 4B8CD 3KDKA 2W76A 4OX9H 2VQFH 4JV5H 3J7AK 2Y3MA 1HNZH 4JTMA 4X66H 4DV4H 4LFAH 1FJGH 2VKCA 3FAUA 4YY3H 4NZTM 2W6TA 1XMQH 4DUYH 4LF4H 3JAMW 1I94H 4JI1H 4DUZH 1XNRH 5LL6b 4JI3H 2UXBH 5IWAH 4DV5H 2UUAH 3T1HH 3ADYA 2UUBH 4GKJH 2D1UA 5BR8H 1N34H 4LF7H 4B3SH 3OSSD 2L4WA 1N32H 2X531 3SB1A 4OCHA 2IAHA 4AQYH 1HNWH 1S03G 4GKKH 2M5JA 4NZRM 2O4CA 1IBMH 4DV1H 3OTOH 2W75A 3OETA 1FKAH 3KDGA 4JI6H 1IBLH
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2W6T A;  2W78 A;  2W77 A;  4E9J A;  2O5P A;  2D1U A;  2W6U A;  2W16 A;  4G08 A;  2A02 A;  3OSS D;  4M0N A;  1ZZV A;  2IAH A;  2W76 A;  2M5J A;  3EZJ A;  2Y3M A;  3GR5 A;  4JTM A;  4EC5 A;  2W75 A;  4M0H A;  4AR0 A; 
#chains in the Genus database with same CATH topology
 4DR3 H;  3T1Y H;  2W78 A;  1PQX A;  2VQE H;  1XMO H;  3L7Z C;  2OPV A;  4JI0 H;  1K28 D;  2ANR A;  2P2R A;  2QND A;  4JI7 H;  1ZZJ A;  1XNQ H;  3QD7 X;  2JEA I;  4DR1 H;  1SEI A;  2YQR A;  2W16 A;  5FLX W;  1UG8 A;  2JEB I;  1HNX H;  4NBQ A;  1HR0 H;  4OD6 A;  1J5E H;  2FMR A;  4JVH A;  4B3T H;  4PDB A;  2LF0 A;  4DR7 H;  4LFB H;  2CPQ A;  2UXD H;  4DR4 H;  1NXU A;  4NXN H;  2BA0 A;  1V8C A;  3GR5 A;  2UUC H;  3GS9 A;  1F0X A;  2CTL A;  4EC5 A;  4DV0 H;  4DR5 H;  3J81 W;  2CWF A;  4LF6 H;  4KHP H;  4M0H A;  2FFM A;  4LFC H;  4AR0 A;  2LTL A;  4MTK A;  2NN6 G;  4DV6 H;  2AXY A;  1ZTG A;  5DT9 A;  4WAL A;  4X65 H;  4DV2 H;  2G8Y A;  4JI4 H;  2UXC H;  1S20 A;  2M6Q A;  2E5L H;  4DV3 H;  4LF5 H;  3KDG A;  3VKE A;  1VIG A;  2D9I A;  2DGR A;  2O5P A;  2HHH H;  1WTJ A;  5A2Q W;  4G08 A;  4FJU A;  2A02 A;  2WZP R;  1X4M A;  2Z6B D;  1EC6 A;  5K36 G;  1IBK H;  4JYA H;  3CDD A;  4WAN A;  3GAB A;  4M0N A;  4UHV A;  2ANN A;  4B3M H;  2PT7 G;  2JA9 A;  2CTM A;  4NXM H;  4JI8 H;  2UU9 H;  1X0A A;  2LTM A;  3EZJ A;  3J80 W;  3RF2 A;  4IFD G;  3U1K A;  1WTH D;  2CTF A;  2M8W A;  2K1H A;  1N36 H;  1X4N A;  4H8A A;  1AN7 A;  4JI5 H;  1ZZV A;  2FPH X;  4X62 H;  1ODH A;  4LF8 H;  1X9Z A;  4X64 H;  4K0K H;  4BA2 I;  2W77 A;  5IT9 W;  2ZQE A;  4E9J A;  3GKU A;  4DR6 H;  1I6U A;  1WRU A;  2JVZ A;  4YHH H;  5LMU H;  1N33 H;  4B3R H;  4DR2 H;  1Z2I A;  3NCV A;  3V69 A;  2ZM6 H;  1WE8 A;  2W6U A;  1DTJ A;  2CPM A;  1VIH A;  1ZZK A;  1V9N A;  5LMN H;  2PQU A;  4JI2 H;  2F4V H;  4DV7 H;  4LF9 H;  1MSZ A;  3I0P A;  3OV5 A;  4B8C D;  2BL5 A;  2HH2 A;  3KDK A;  2W76 A;  2CTE A;  4OX9 H;  2VQF H;  1XRH A;  4JV5 H;  1DT4 A;  4BA1 I;  3J7A K;  1TUA A;  4LIJ A;  2Y3M A;  1HNZ H;  5C0X G;  4X66 H;  4JTM A;  4DV4 H;  4LFA H;  1FJG H;  2VKC A;  3D37 A;  5JEA G;  1KHM A;  3FAU A;  4YY3 H;  1VBI A;  4NZT M;  4JVY A;  2W6T A;  1XMQ H;  4DUY H;  4LF4 H;  3JAM W;  2A1S A;  2CTJ A;  2MJH A;  2CWH A;  1I94 H;  4JI1 H;  4DUZ H;  2E3U A;  1ZZI A;  4AIM A;  5LL6 b;  4JI3 H;  1XNR H;  3AEV B;  5IWA H;  1WVN A;  4DV5 H;  2UUA H;  3T1H H;  2UXB H;  2UUB H;  3ADY A;  4GKJ H;  2D1U A;  2OPU A;  5BR8 H;  1N34 H;  2JZX A;  4LF7 H;  4B3S H;  3OSS D;  4B8T A;  2L4W A;  4AM3 A;  2X06 A;  2JE6 I;  1J4W A;  4FJS A;  1J5K A;  1N32 H;  2PY9 A;  2Z0S A;  4OCH A;  3SB1 A;  4OO1 G;  2X53 1;  2IAH A;  4AQY H;  1HNW H;  1S03 G;  1K1G A;  2CTK A;  4GKK H;  2M5J A;  2P5Z X;  4NZR M;  4QMF B;  1WHR A;  2O4C A;  1IBM H;  2HH3 A;  3OTO H;  4DV1 H;  2W75 A;  3OET A;  1FKA H;  3UOE A;  2LRR A;  4JI6 H;  1IBL H; 
#chains in the Genus database with same CATH homology
 4DR3 H;  3T1Y H;  2W78 A;  1XMO H;  2VQE H;  4JI0 H;  1K28 D;  4JI7 H;  1XNQ H;  3QD7 X;  4DR1 H;  1SEI A;  2W16 A;  5FLX W;  1HNX H;  1HR0 H;  4OD6 A;  1J5E H;  4B3T H;  4PDB A;  2LF0 A;  4DR7 H;  4LFB H;  2UXD H;  4DR4 H;  4NXN H;  3GR5 A;  2UUC H;  3GS9 A;  1F0X A;  4EC5 A;  4DV0 H;  4DR5 H;  4LF6 H;  3J81 W;  4KHP H;  4M0H A;  4LFC H;  4AR0 A;  4DV6 H;  5DT9 A;  4DV2 H;  4X65 H;  4JI4 H;  2UXC H;  2E5L H;  4DV3 H;  4LF5 H;  2D9I A;  2O5P A;  2HHH H;  5A2Q W;  4G08 A;  2A02 A;  2WZP R;  2Z6B D;  1IBK H;  4JYA H;  3GAB A;  4M0N A;  4B3M H;  2PT7 G;  4NXM H;  4JI8 H;  2UU9 H;  3EZJ A;  3J80 W;  3RF2 A;  1WTH D;  1N36 H;  1ZZV A;  1AN7 A;  4JI5 H;  2FPH X;  4X62 H;  1ODH A;  4LF8 H;  1X9Z A;  4X64 H;  4K0K H;  2W77 A;  5IT9 W;  2ZQE A;  4E9J A;  4DR6 H;  1I6U A;  4YHH H;  5LMU H;  1N33 H;  4B3R H;  4DR2 H;  3NCV A;  2ZM6 H;  2W6U A;  5LMN H;  4JI2 H;  2F4V H;  4DV7 H;  4LF9 H;  3OV5 A;  4B8C D;  3KDK A;  2W76 A;  4OX9 H;  2VQF H;  4JV5 H;  3J7A K;  2Y3M A;  1HNZ H;  4JTM A;  4X66 H;  4DV4 H;  4LFA H;  1FJG H;  2VKC A;  3FAU A;  4YY3 H;  4NZT M;  2W6T A;  1XMQ H;  4DUY H;  4LF4 H;  3JAM W;  1I94 H;  4JI1 H;  4DUZ H;  1XNR H;  5LL6 b;  4JI3 H;  2UXB H;  5IWA H;  4DV5 H;  2UUA H;  3T1H H;  3ADY A;  2UUB H;  4GKJ H;  2D1U A;  5BR8 H;  1N34 H;  4LF7 H;  4B3S H;  3OSS D;  2L4W A;  1N32 H;  2X53 1;  3SB1 A;  4OCH A;  2IAH A;  4AQY H;  1HNW H;  1S03 G;  4GKK H;  2M5J A;  4NZR M;  2O4C A;  1IBM H;  4DV1 H;  3OTO H;  2W75 A;  3OET A;  1FKA H;  3KDG A;  4JI6 H;  1IBL H; 
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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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