2AGYD

Crystal structure of the schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (aadh) with tryptamine. monoclinic form
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Note, that the numbers in the matrix denote the consecutive residues in the loop, not the index of amino acids in the chain!
Knot K 1x +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
+ 31 16-74 59 1-15, 75-82 15 8 knot
Fingerprint Knot forming loop Loop type
K +31 Glu71 ... Cys75 <-> Cys140 ... Cys113 <-> Cys81 ... Trq109 <-> Trp160 ...
Chain closureLeu179 <-> Glu71
 probabilistic
Chain Sequence
EVNSCDYWRHCAVDGFLCSCCGGTTTTCPPGSTPSPIS-IGTCHNPHDGKDYLISYHDCCGKTACGRCQCNTQTRERPGYEFFLHNDVNWCMANENSTFHCTTSVLVGL
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
sequence length 109
structure length 108
publication title Atomic description of an enzyme reaction dominated by proton tunneling
pubmed doi rcsb
molecule tags Oxidoreductase
molecule keywords Aromatic amine dehydrogenase
missing residues 39
total genus Genus: 27
ec nomenclature ec 1.4.9.2: Aralkylamine dehydrogenase (azurin).
pdb deposition date 2005-07-27
KnotProt deposition date 2018-10-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF02975 Me-amine-dh_L Methylamine dehydrogenase, L chain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.60.30.10 Mainly Beta Sandwich Electron Transport Ethylamine Dehydrogenase Electron Transport Ethylamine Dehydrogenase 2agyD00
2.60.30.10 Mainly Beta Sandwich Electron Transport Ethylamine Dehydrogenase Electron Transport Ethylamine Dehydrogenase 2agyD00
3L4OC 2IUPD 2HJ4D 2H47B 2AH0D 2IUVD 2Q7QD 2AGLD 1MDAM 2GC7B 2IURD 2J57K 2OJYD 1MG3B 2I0SD 2OIZD 2H3XB 2HKMD 2MTAL 2HJBD 2J55L 2J56L 2AH1D 2MADL 2AGXD 2HXCD 2HKRD 2AGWD 2GC4B 2IAAB 2AGYD 3C75L 2BBKL 1MG2B 2OK4D 2I0TD 2IUQD
chains in the KnotProt database with same CATH superfamily
3L4OC 2IUPD 2HJ4D 2H47B 2AH0D 2IUVD 2Q7QD 2AGLD 1MDAM 2GC7B 2IURD 2J57K 2OJYD 1MG3B 2I0SD 2OIZD 2H3XB 2HKMD 2MTAL 2HJBD 2J55L 2J56L 2AH1D 2MADL 2AGXD 2HXCD 2HKRD 2AGWD 2GC4B 2IAAB 2AGYD 3C75L 2BBKL 1MG2B 2OK4D 2I0TD 2IUQD
chains in the KnotProt database with same CATH topology
3L4OC 2IUPD 2HJ4D 2H47B 2AH0D 2IUVD 2Q7QD 2AGLD 1MDAM 2GC7B 2IURD 2J57K 2OJYD 1MG3B 2I0SD 2OIZD 2H3XB 2HKMD 2MTAL 2HJBD 2J55L 2J56L 2AH1D 2MADL 2AGXD 2HXCD 2HKRD 2AGWD 2GC4B 2IAAB 2AGYD 3C75L 2BBKL 1MG2B 2OK4D 2I0TD 2IUQD
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 3L4O C;  2IUP D;  2HJ4 D;  2H47 B;  2AH0 D;  2IUV D;  2Q7Q D;  2AGL D;  1MDA M;  2GC7 B;  2IUR D;  2J57 K;  2OJY D;  1MG3 B;  2I0S D;  2OIZ D;  2H3X B;  2HKM D;  2MTA L;  2HJB D;  2J55 L;  2J56 L;  2AH1 D;  2MAD L;  2AGX D;  2HXC D;  2HKR D;  2AGW D;  2GC4 B;  2IAA B;  2AGY D;  3C75 L;  2BBK L;  1MG2 B;  2OK4 D;  2I0T D;  2IUQ D; 
#chains in the KnotProt database with same CATH topology
 3L4O C;  2IUP D;  2HJ4 D;  2H47 B;  2AH0 D;  2IUV D;  2Q7Q D;  2AGL D;  1MDA M;  2GC7 B;  2IUR D;  2J57 K;  2OJY D;  1MG3 B;  2I0S D;  2OIZ D;  2H3X B;  2HKM D;  2MTA L;  2HJB D;  2J55 L;  2J56 L;  2AH1 D;  2MAD L;  2AGX D;  2HXC D;  2HKR D;  2AGW D;  2GC4 B;  2IAA B;  2AGY D;  3C75 L;  2BBK L;  1MG2 B;  2OK4 D;  2I0T D;  2IUQ D; 
#chains in the KnotProt database with same CATH homology
 3L4O C;  2IUP D;  2HJ4 D;  2H47 B;  2AH0 D;  2IUV D;  2Q7Q D;  2AGL D;  1MDA M;  2GC7 B;  2IUR D;  2J57 K;  2OJY D;  1MG3 B;  2I0S D;  2OIZ D;  2H3X B;  2HKM D;  2MTA L;  2HJB D;  2J55 L;  2J56 L;  2AH1 D;  2MAD L;  2AGX D;  2HXC D;  2HKR D;  2AGW D;  2GC4 B;  2IAA B;  2AGY D;  3C75 L;  2BBK L;  1MG2 B;  2OK4 D;  2I0T D;  2IUQ D;
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling