1J3GA

Solution structure of citrobacter freundii ampd
Total Genus 30
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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
30
sequence length
187
structure length
187
Chain Sequence
MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTPSSHKEMT
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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 Hydrolase
molecule keywords AmpD protein
publication title NMR Structure of Citrobacter freundii AmpD, Comparison with Bacteriophage T7 Lysozyme and Homology with PGRP Domains
pubmed doi rcsb
source organism Citrobacter freundii
total genus 30
structure length 187
sequence length 187
ec nomenclature ec 3.5.1.28: N-acetylmuramoyl-L-alanine amidase.
pdb deposition date 2003-01-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01510 Amidase_2 N-acetylmuramoyl-L-alanine amidase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.80.10 Alpha Beta 3-Layer(aba) Sandwich Lysozyme-like Peptidoglycan recognition protein-like 1j3gA00
1YB0A 3UILA 4OLSA 3QV4A 1SXRA 4BJ4A 3TRUA 3NG4A 4ORVA 1TWQA 4Q8SA 3T39A 2AR3A 4BXEA 3QJ1A 2F2LA 4OPPA 1LBAA 5CTVA 3CXAA 2RKQA 4X36A 5E0AA 4GF9A 2APHA 2F2LX 3T2VA 1SK3A 4ZXMA 2WKXA 2Y2EA 1Z6IA 4KNLA 4BOLA 3RT4A 2L47A 3USXA 3C2XA 3NNOA 1OHTA 4Q9EA 1YCKA 3HMBA 4FNNA 4KNKA 3UMQA 3RDRA 3CORA 3UMLA 2Y2DA 2EAXA 3D2ZA 2EAVA 2XZ8A 4BXDA 4IVVA 4OUGA 4BXJA 2BH7A 4BPAA 3LATA 2Y2CA 3OGXA 3NW3A 3EP1A 3QS0A 5DWFA 1S2JA 3CG9A 2Y28A 1SK4A 2R90A 2CB3A 2XZ4A 3D2YA 1AROL 2R2KA 2Y2BA 5E0BA 1J3GA 4Z8IA 3O4KA 2Z9NA
chains in the Genus database with same CATH superfamily
1YB0A 3UILA 4OLSA 3QV4A 1SXRA 4BJ4A 3TRUA 3NG4A 4ORVA 1TWQA 4Q8SA 3T39A 2AR3A 4BXEA 3QJ1A 2F2LA 4OPPA 1LBAA 5CTVA 3CXAA 2RKQA 4X36A 5E0AA 4GF9A 2APHA 2F2LX 3T2VA 1SK3A 4ZXMA 2WKXA 2Y2EA 1Z6IA 4KNLA 4BOLA 3RT4A 2L47A 3USXA 3C2XA 3NNOA 1OHTA 4Q9EA 1YCKA 3HMBA 4FNNA 4KNKA 3UMQA 3RDRA 3CORA 3UMLA 2Y2DA 2EAXA 3D2ZA 2EAVA 2XZ8A 4BXDA 4IVVA 4OUGA 4BXJA 2BH7A 4BPAA 3LATA 2Y2CA 3OGXA 3NW3A 3EP1A 3QS0A 5DWFA 1S2JA 3CG9A 2Y28A 1SK4A 2R90A 2CB3A 2XZ4A 3D2YA 1AROL 2R2KA 2Y2BA 5E0BA 1J3GA 4Z8IA 3O4KA 2Z9NA
chains in the Genus database with same CATH topology
1YB0A 3UILA 4OLSA 3QV4A 1SXRA 4BJ4A 3TRUA 3NG4A 4ORVA 1TWQA 4Q8SA 3T39A 2AR3A 4BXEA 3QJ1A 2F2LA 4OPPA 1LBAA 5CTVA 3CXAA 2RKQA 4X36A 5E0AA 4GF9A 2APHA 2F2LX 3T2VA 1SK3A 4ZXMA 2WKXA 2Y2EA 1Z6IA 4KNLA 4BOLA 3RT4A 2L47A 3USXA 3C2XA 3NNOA 1OHTA 4Q9EA 1YCKA 3HMBA 4FNNA 4KNKA 3UMQA 3RDRA 3CORA 3UMLA 2Y2DA 2EAXA 3D2ZA 2EAVA 2XZ8A 4BXDA 4IVVA 4OUGA 4BXJA 2BH7A 4BPAA 3LATA 2Y2CA 3OGXA 3NW3A 3EP1A 3QS0A 5DWFA 1S2JA 3CG9A 2Y28A 1SK4A 2R90A 2CB3A 2XZ4A 3D2YA 1AROL 2R2KA 2Y2BA 5E0BA 1J3GA 4Z8IA 3O4KA 2Z9NA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1YB0 A;  3UIL A;  4OLS A;  3QV4 A;  1SXR A;  4BJ4 A;  3TRU A;  3NG4 A;  4ORV A;  1TWQ A;  4Q8S A;  3T39 A;  2AR3 A;  4BXE A;  3QJ1 A;  2F2L A;  4OPP A;  1LBA A;  5CTV A;  3CXA A;  2RKQ A;  4X36 A;  5E0A A;  4GF9 A;  2APH A;  2F2L X;  3T2V A;  1SK3 A;  4ZXM A;  2WKX A;  2Y2E A;  1Z6I A;  4KNL A;  4BOL A;  3RT4 A;  2L47 A;  3USX A;  3C2X A;  3NNO A;  1OHT A;  4Q9E A;  1YCK A;  3HMB A;  4FNN A;  4KNK A;  3UMQ A;  3RDR A;  3COR A;  3UML A;  2Y2D A;  2EAX A;  3D2Z A;  2EAV A;  2XZ8 A;  4BXD A;  4IVV A;  4OUG A;  4BXJ A;  2BH7 A;  4BPA A;  3LAT A;  2Y2C A;  3OGX A;  3NW3 A;  3EP1 A;  3QS0 A;  5DWF A;  1S2J A;  3CG9 A;  2Y28 A;  1SK4 A;  2R90 A;  2CB3 A;  2XZ4 A;  3D2Y A;  1ARO L;  2R2K A;  2Y2B A;  5E0B A;  1J3G A;  4Z8I A;  3O4K A;  2Z9N A; 
#chains in the Genus database with same CATH topology
 1YB0 A;  3UIL A;  4OLS A;  3QV4 A;  1SXR A;  4BJ4 A;  3TRU A;  3NG4 A;  4ORV A;  1TWQ A;  4Q8S A;  3T39 A;  2AR3 A;  4BXE A;  3QJ1 A;  2F2L A;  4OPP A;  1LBA A;  5CTV A;  3CXA A;  2RKQ A;  4X36 A;  5E0A A;  4GF9 A;  2APH A;  2F2L X;  3T2V A;  1SK3 A;  4ZXM A;  2WKX A;  2Y2E A;  1Z6I A;  4KNL A;  4BOL A;  3RT4 A;  2L47 A;  3USX A;  3C2X A;  3NNO A;  1OHT A;  4Q9E A;  1YCK A;  3HMB A;  4FNN A;  4KNK A;  3UMQ A;  3RDR A;  3COR A;  3UML A;  2Y2D A;  2EAX A;  3D2Z A;  2EAV A;  2XZ8 A;  4BXD A;  4IVV A;  4OUG A;  4BXJ A;  2BH7 A;  4BPA A;  3LAT A;  2Y2C A;  3OGX A;  3NW3 A;  3EP1 A;  3QS0 A;  5DWF A;  1S2J A;  3CG9 A;  2Y28 A;  1SK4 A;  2R90 A;  2CB3 A;  2XZ4 A;  3D2Y A;  1ARO L;  2R2K A;  2Y2B A;  5E0B A;  1J3G A;  4Z8I A;  3O4K A;  2Z9N A; 
#chains in the Genus database with same CATH homology
 1YB0 A;  3UIL A;  4OLS A;  3QV4 A;  1SXR A;  4BJ4 A;  3TRU A;  3NG4 A;  4ORV A;  1TWQ A;  4Q8S A;  3T39 A;  2AR3 A;  4BXE A;  3QJ1 A;  2F2L A;  4OPP A;  1LBA A;  5CTV A;  3CXA A;  2RKQ A;  4X36 A;  5E0A A;  4GF9 A;  2APH A;  2F2L X;  3T2V A;  1SK3 A;  4ZXM A;  2WKX A;  2Y2E A;  1Z6I A;  4KNL A;  4BOL A;  3RT4 A;  2L47 A;  3USX A;  3C2X A;  3NNO A;  1OHT A;  4Q9E A;  1YCK A;  3HMB A;  4FNN A;  4KNK A;  3UMQ A;  3RDR A;  3COR A;  3UML A;  2Y2D A;  2EAX A;  3D2Z A;  2EAV A;  2XZ8 A;  4BXD A;  4IVV A;  4OUG A;  4BXJ A;  2BH7 A;  4BPA A;  3LAT A;  2Y2C A;  3OGX A;  3NW3 A;  3EP1 A;  3QS0 A;  5DWF A;  1S2J A;  3CG9 A;  2Y28 A;  1SK4 A;  2R90 A;  2CB3 A;  2XZ4 A;  3D2Y A;  1ARO L;  2R2K A;  2Y2B A;  5E0B A;  1J3G A;  4Z8I A;  3O4K A;  2Z9N 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)

 
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#similar chains, but unknotted
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