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


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