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Asym./Biol. Unit (Jmol Viewer)

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Title :   L-AMINO ACID OXIDASE FROM AGKISTRODON HALYS IN COMPLEX WITH SUICIDE SUBSTRATE L-VINYLGLYCINE

Authors :   H. Zhang, M. Teng, L. Niu

Date :   22 May 04 (Deposition) - 22 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Complex Structure With Suicide Substrate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhang, M. Teng, L. Niu
Structures Of L-Amino Acid Oxidase In Complexes With Substrates And Substrate Analogue
To Be Published
PubMed: search

Molecule 1 - L-AMINO ACID OXIDASE
	Chains	:	A
	EC Number	:	1.4.3.2
	Organism Common	:	HALYS VIPER
	Organism Scientific	:	GLOYDIUS HALYS
	Organism Taxid	:	8714
	Synonym	:	AHLAAO

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	LVG	2	Ligand/Ion	L-VINYLGLYCINE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:172	BINDING SITE FOR RESIDUE NAG A 489
2	AC2	SOFTWARE	HIS A:342 , ASN A:359 , ASN A:361	BINDING SITE FOR RESIDUE NDG A 490
3	AC3	SOFTWARE	VAL A:39 , GLY A:40 , GLY A:42 , SER A:44 , LEU A:62 , GLU A:63 , ALA A:64 , GLY A:70 , ARG A:71 , GLY A:87 , PRO A:88 , MET A:89 , ARG A:90 , ALA A:259 , VAL A:261 , CYS A:293 , THR A:294 , TYR A:372 , TRP A:420 , GLY A:429 , ILE A:430 , GLU A:457 , GLY A:464 , TRP A:465 , ILE A:466 , THR A:469 , HOH A:494 , HOH A:500 , HOH A:504 , HOH A:525	BINDING SITE FOR RESIDUE FAD A 488
4	AC4	SOFTWARE	ARG A:90 , ASN A:208 , HIS A:223 , TYR A:356 , LVG A:491	BINDING SITE FOR RESIDUE LVG A 487
5	AC5	SOFTWARE	ARG A:90 , PHE A:227 , TYR A:372 , LVG A:487 , HOH A:525	BINDING SITE FOR RESIDUE LVG A 491

Asymmetric/Biological Unit

No.	Residues
1	A:10	-	A:173
2	A:331	-	A:412

Asymmetric/Biological Unit

No.	Residues
1	Glu A:305	-	Pro A:306

(no "SAP(SNP)/Variant" information available for 1TDK)

(no "PROSITE Motif" information available for 1TDK)

(no "Exon" information available for 1TDK)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:484
 aligned with OXLA_GLOBL | Q90W54 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:484
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500    
           OXLA_GLOBL    21 DRNPLEECFRETDYEEFLEIARNGLKATSNPKHVVIVGAGMSGLSAAYVLSGAGHQVTVLEASERAGGRVRTYRNDKEGWYANLGPMRLPEKHRIVREYIRKFGLQLNEFSQENDNAWYFIKNIRKRVGEVKKDPGVLKYPVKPSEEGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLLKEGNLSPGAVDMIGDLMNEDSGYYVSFPESLRHDDIFAYEKRFDEIVGGMDKLPTSMYRAIEEKVHLNAQVIKIQKNAEKVTVVYQTPAKEMASVTADYVIVCTTSRATRRIKFEPPLPPKKAHALRSVHYRSGTKIFLTCTKKFWEDEGIHGGKSTTDLPSRFIYYPNHNFTSGVGVIIAYGIGDDANFFQALDFKDCADIVINDLSLIHQLPREEIQTFCYPSMIQKWSLDKYAMGGITTFTPYQFQHFSEPLTASVDRIYFAGEHTAEAHGWIDSTIKSGLRAARDVNRASEQ 504
               SCOP domains d1tdka1 A:3-319,A:433-486 L-aminoacid oxidase                                                                                                                                                                                                                                                                                d1tdka2 A:320-432 L-aminoacid oxidase                                                                            d1tdka1 A:3-319,A:433-486 L-aminoacid oxidase          SCOP domains
               CATH domains -1tdkA01               ---------1tdkA02                       --------1tdkA01 A:4-25,A:73-129,A:233-236,A:324-420              1tdkA03 A:130-230 Guanine Nucleotide Dissociation Inhibitor, domain 1                                --1tdk-----1tdkA02 A:35-64,A:242-318,A:446-486  [code=3.50.50.60, no name defined]      -----1tdkA01 A:4-25,A:73-129,A:233-236,A:324-420  [code=3.90.660.10, no name defined]                 -------------------------1tdkA02 A:35-64,A:242-318,A:446-486       CATH domains
               Pfam domains ----------------------------------------Amino_oxidase-1tdkA01 A:43-481                                                                                                                                                                                                                                                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeee...........eeee....eeee.....ee..hhhhhhhhhhh...eeee.......eeee..eeeehhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...ee...eeeeeeee..eeeeeee.....eeeeee.eeee..hhhhhh..eee...hhhhhhhhhhh.ee.eeeeeeee..hhhhhhh....eeee.....eee..........eeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee.hhh......ee....hhhhhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tdk A   3 DRNPLEECFRETDYEEFLEIARNGLKATSNPKHVVVVGAGMSGLSAAYVLSGAGHQVTVLEASERAGGRVRTYRNDKEDWYANLGPMRLPEKHRIVREYIRKFGLQLNEFSQENDNAWYFIKNIRKRVGEVKKDPGVLKYPVKPSEEGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLLKEGNLSPGAVDMIGDLMNEDSGYYVSFPESLRHDDIFAYEKRFDEIVGGMDKLPTSMYRAIEEKVHLNAQVIKIQKNAEKVTVVYQTPAKEMASVTADYVIVCTTSRATRRIKFEPPLPPKKAHALRSVHYRSGTKIFLTCTKKFWEDEGIHGGKSTTDLPSRFIYYPNHNFTSGVGVIIAYGIGDDANFFQALDFKDCADIVINDLSLIHQLPREEIQTFCYPSMIQKWSLDKYAMGGITTFTPYQFQHFSESLTASVDRIYFAGEHTAEAHGWIDSTIKSGLRAARDVNRASEQ 486
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482

Chain A from PDB  Type:PROTEIN  Length:484
 aligned with OXLA_GLOHA | Q6STF1 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:484
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500    
           OXLA_GLOHA    21 DRNPLEECFRETDYEEFLEIARNGLKATSNPKHVVVVGAGMSGLSAAYVLSGAGHQVTVLEASERAGGRVRTYRNDKEDWYANLGPMRLPEKHRIVREYIRKFGLQLNEFSQENDNAWYFIKNIRKRVGEVKKDPGVLKYPVKPSEEGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLLKEGNLSPGAVDMIGDLMNEDSGYYVSFPESLRHDDIFAYEKRFDEIVGGMDKLPTSMYRAIEEKVHLNAQVIKIQKNAEKVTVVYQTPAKEMASVTADYVIVCTTSRATRRIKFEPPLPPKKAHALRSVHYRSGTKIFLTCTKKFWEDEGIHGGKSTTDLPSRFIYYPNHNFTSGVGVIIAYGIGDDANFFQALDFKDCADIVINDLSLIHQLPREEIQTFCYPSMIQKWSLDKYAMGGITTFTPYQFQHFSESLTASVDRIYFAGEHTAEAHGWIDSTIKSGLRAARDVNRASEQ 504
               SCOP domains d1tdka1 A:3-319,A:433-486 L-aminoacid oxidase                                                                                                                                                                                                                                                                                d1tdka2 A:320-432 L-aminoacid oxidase                                                                            d1tdka1 A:3-319,A:433-486 L-aminoacid oxidase          SCOP domains
               CATH domains -1tdkA01               ---------1tdkA02                       --------1tdkA01 A:4-25,A:73-129,A:233-236,A:324-420              1tdkA03 A:130-230 Guanine Nucleotide Dissociation Inhibitor, domain 1                                --1tdk-----1tdkA02 A:35-64,A:242-318,A:446-486  [code=3.50.50.60, no name defined]      -----1tdkA01 A:4-25,A:73-129,A:233-236,A:324-420  [code=3.90.660.10, no name defined]                 -------------------------1tdkA02 A:35-64,A:242-318,A:446-486       CATH domains
               Pfam domains ----------------------------------------Amino_oxidase-1tdkA01 A:43-481                                                                                                                                                                                                                                                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh..eeeee...........eeee....eeee.....ee..hhhhhhhhhhh...eeee.......eeee..eeeehhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhh....eeee....hhhhhhhhhhh...ee...eeeeeeee..eeeeeee.....eeeeee.eeee..hhhhhh..eee...hhhhhhhhhhh.ee.eeeeeeee..hhhhhhh....eeee.....eee..........eeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee.hhh......ee....hhhhhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tdk A   3 DRNPLEECFRETDYEEFLEIARNGLKATSNPKHVVVVGAGMSGLSAAYVLSGAGHQVTVLEASERAGGRVRTYRNDKEDWYANLGPMRLPEKHRIVREYIRKFGLQLNEFSQENDNAWYFIKNIRKRVGEVKKDPGVLKYPVKPSEEGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLLKEGNLSPGAVDMIGDLMNEDSGYYVSFPESLRHDDIFAYEKRFDEIVGGMDKLPTSMYRAIEEKVHLNAQVIKIQKNAEKVTVVYQTPAKEMASVTADYVIVCTTSRATRRIKFEPPLPPKKAHALRSVHYRSGTKIFLTCTKKFWEDEGIHGGKSTTDLPSRFIYYPNHNFTSGVGVIIAYGIGDDANFFQALDFKDCADIVINDLSLIHQLPREEIQTFCYPSMIQKWSLDKYAMGGITTFTPYQFQHFSESLTASVDRIYFAGEHTAEAHGWIDSTIKSGLRAARDVNRASEQ 486
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Amino_oxidase (60)

Gloydius halys (Chinese water mocassin) (Agkistrodon halys) (4)

Amino_oxidase-1tdkA01

A:43-481

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OXLA_GLOBL | Q90W54)

molecular function
	GO:0001716	L-amino-acid oxidase activity	Catalysis of the reaction: a L-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (OXLA_GLOHA | Q6STF1)

molecular function
	GO:0001716	L-amino-acid oxidase activity	Catalysis of the reaction: a L-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:305 - Pro A:306	[ RasMol ]

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1tdn	L-AMINO ACID OXIDASE IN COMPLEX WITH L-LEUCINE
1tdo	L-AMINO ACID OXIDASE IN COMPLEX WITH L-PHENYLALANINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

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