2Y2CA

Crystal structure of ampd apoenzyme
Total Genus 60
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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
60
sequence length
179
structure length
179
Chain Sequence
LLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTP
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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 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
publication title Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.
pubmed doi rcsb
source organism Citrobacter freundii
total genus 60
structure length 179
sequence length 179
chains with identical sequence B, C
ec nomenclature ec 3.5.1.28: N-acetylmuramoyl-L-alanine amidase.
pdb deposition date 2010-12-14

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 2y2cA00
3NNOA 1SK3A 1SXRA 2EAXA 2Y2DA 1OHTA 3QJ1A 2Y28A 4Q9EA 4BXEA 2Y2BA 4BXDA 2F2LX 3NW3A 2L47A 3LATA 2APHA 3USXA 3D2ZA 4ORVA 3RDRA 1AROL 4OPPA 4OUGA 3TRUA 1J3GA 3HMBA 3CXAA 3UMLA 5E0AA 1S2JA 3UILA 1LBAA 4KNKA 4OLSA 2WKXA 5CTVA 2Y2CA 1TWQA 5DWFA 2BH7A 4BXJA 2Y2EA 1SK4A 3O4KA 4BOLA 3CORA 4X36A 4FNNA 1YB0A 4ZXMA 4Z8IA 2AR3A 5E0BA 4Q8SA 2F2LA 2XZ4A 2XZ8A 1Z6IA 3T2VA 4GF9A 4KNLA 3QV4A 3UMQA 3OGXA 3D2YA 2CB3A 2R90A 3C2XA 4BJ4A 3T39A 2Z9NA 3QS0A 4IVVA 2EAVA 2R2KA 2RKQA 1YCKA 3NG4A 4BPAA 3EP1A 3CG9A 3RT4A
chains in the Genus database with same CATH superfamily
3NNOA 1SK3A 1SXRA 2EAXA 2Y2DA 1OHTA 3QJ1A 2Y28A 4Q9EA 4BXEA 2Y2BA 4BXDA 2F2LX 3NW3A 2L47A 3LATA 2APHA 3USXA 3D2ZA 4ORVA 3RDRA 1AROL 4OPPA 4OUGA 3TRUA 1J3GA 3HMBA 3CXAA 3UMLA 5E0AA 1S2JA 3UILA 1LBAA 4KNKA 4OLSA 2WKXA 5CTVA 2Y2CA 1TWQA 5DWFA 2BH7A 4BXJA 2Y2EA 1SK4A 3O4KA 4BOLA 3CORA 4X36A 4FNNA 1YB0A 4ZXMA 4Z8IA 2AR3A 5E0BA 4Q8SA 2F2LA 2XZ4A 2XZ8A 1Z6IA 3T2VA 4GF9A 4KNLA 3QV4A 3UMQA 3OGXA 3D2YA 2CB3A 2R90A 3C2XA 4BJ4A 3T39A 2Z9NA 3QS0A 4IVVA 2EAVA 2R2KA 2RKQA 1YCKA 3NG4A 4BPAA 3EP1A 3CG9A 3RT4A
chains in the Genus database with same CATH topology
3NNOA 1SK3A 1SXRA 2EAXA 2Y2DA 1OHTA 3QJ1A 2Y28A 4Q9EA 4BXEA 2Y2BA 4BXDA 2F2LX 3NW3A 2L47A 3LATA 2APHA 3USXA 3D2ZA 4ORVA 3RDRA 1AROL 4OPPA 4OUGA 3TRUA 1J3GA 3HMBA 3CXAA 3UMLA 5E0AA 1S2JA 3UILA 1LBAA 4KNKA 4OLSA 2WKXA 5CTVA 2Y2CA 1TWQA 5DWFA 2BH7A 4BXJA 2Y2EA 1SK4A 3O4KA 4BOLA 3CORA 4X36A 4FNNA 1YB0A 4ZXMA 4Z8IA 2AR3A 5E0BA 4Q8SA 2F2LA 2XZ4A 2XZ8A 1Z6IA 3T2VA 4GF9A 4KNLA 3QV4A 3UMQA 3OGXA 3D2YA 2CB3A 2R90A 3C2XA 4BJ4A 3T39A 2Z9NA 3QS0A 4IVVA 2EAVA 2R2KA 2RKQA 1YCKA 3NG4A 4BPAA 3EP1A 3CG9A 3RT4A
chains in the Genus database with same CATH homology


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