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


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