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


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