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


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