3EZJA

Crystal structure of the n-terminal domain of the secretin gspd from etec determined with the assistance of a nanobody
Total Genus 58
Loading diagram...

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...