3GDP - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HYDROXYNITRILE LYASE FROM ALMOND, MONOCLINIC CRYSTAL FORM

Authors :   I. Dreveny, K. Gruber, C. Kratky

Date :   24 Feb 09 (Deposition) - 24 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.57

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydroxynitrile Lyase, Flavin, Gmc Oxidoreductase, Almond, Cyanogenesis, Flavoprotein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Dreveny, A. S. Andryushkova, A. Glieder, K. Gruber, C. Kratky
Substrate Binding In The Fad-Dependent Hydroxynitrile Lyase From Almond Provides Insight Into The Mechanism Of Cyanohydrin Formation And Explains The Absence Of Dehydrogenation Activity.
Biochemistry V. 48 3370 2009
PubMed-ID: 19256550 | Reference-DOI: 10.1021/BI802162S

Molecule 1 - R-OXYNITRILE LYASE ISOENZYME 1
	Chains	:	A, B
	EC Number	:	4.1.2.10
	Organism Common	:	SWEET ALMOND
	Organism Scientific	:	PRUNUS DULCIS
	Organism Taxid	:	3755

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (8, 25)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
4	FUL	1	Ligand/Ion	BETA-L-FUCOSE
5	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
6	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	11	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (6, 12)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	FUL	1	Ligand/Ion	BETA-L-FUCOSE
5	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (7, 13)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	FUL	-1	Ligand/Ion	BETA-L-FUCOSE
5	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:121 , SER A:125 , PHE A:490 , TYR A:492 , HOH A:866 , HOH A:1156 , HOH A:1176	BINDING SITE FOR RESIDUE IPA A 522
02	AC2	SOFTWARE	GLY A:33 , GLY A:35 , THR A:36 , SER A:37 , LEU A:54 , GLU A:55 , ARG A:56 , VAL A:98 , GLY A:100 , ARG A:101 , VAL A:102 , GLY A:105 , THR A:106 , ASN A:110 , ALA A:111 , GLY A:112 , VAL A:113 , ALA A:215 , VAL A:217 , SER A:256 , ALA A:257 , VAL A:379 , TRP A:458 , HIS A:459 , ASP A:486 , GLY A:487 , HIS A:497 , PRO A:498 , GLN A:499 , TYR A:502 , HOH A:593 , HOH A:694 , HOH A:777 , HOH A:831 , HOH A:835 , HOH A:845 , HOH A:853 , HOH A:879 , HOH A:920	BINDING SITE FOR RESIDUE FAD A 523
03	AC3	SOFTWARE	ASN A:118 , HIS A:177 , GLU A:179 , ASN A:323 , HOH A:632 , HOH A:827 , HOH A:925 , HOH A:1202 , HOH A:1299 , HOH A:1349	BINDING SITE FOR RESIDUE NAG A 524
04	AC4	SOFTWARE	ARG A:116 , ASP A:132 , ASN A:135 , ASP A:176 , NAG A:526 , FUL A:527 , HOH A:568 , HOH A:877 , HOH A:1088 , HOH A:1208 , HOH A:1213 , HOH A:1250	BINDING SITE FOR RESIDUE NAG A 525
05	AC5	SOFTWARE	THR A:119 , ASP A:176 , NAG A:525 , FUL A:527 , MAN A:528 , HOH A:538	BINDING SITE FOR RESIDUE NAG A 526
06	AC6	SOFTWARE	NAG A:525 , NAG A:526 , HOH A:568	BINDING SITE FOR RESIDUE FUL A 527
07	AC7	SOFTWARE	NAG A:526 , MAN A:529 , HOH A:554	BINDING SITE FOR RESIDUE MAN A 528
08	AC8	SOFTWARE	HIS A:171 , GLU A:178 , MAN A:528 , HOH A:588	BINDING SITE FOR RESIDUE MAN A 529
09	AC9	SOFTWARE	LEU A:366 , ASN A:392 , NAG A:531 , FUC A:532 , HOH A:587 , HOH A:683 , HOH A:784	BINDING SITE FOR RESIDUE NAG A 530
10	BC1	SOFTWARE	NAG A:530 , FUC A:532 , HOH A:686	BINDING SITE FOR RESIDUE NAG A 531
11	BC2	SOFTWARE	NAG A:530 , NAG A:531 , HOH A:683	BINDING SITE FOR RESIDUE FUC A 532
12	BC3	SOFTWARE	ASN A:352 , ASN A:430 , HOH A:570 , HOH A:650 , HOH A:824 , HOH A:1301	BINDING SITE FOR RESIDUE NAG A 533
13	BC4	SOFTWARE	ILE B:121 , PHE B:490 , TYR B:492 , HOH B:850 , HOH B:1002 , HOH B:1381	BINDING SITE FOR RESIDUE IPA B 522
14	BC5	SOFTWARE	GLY B:33 , GLY B:35 , THR B:36 , SER B:37 , LEU B:54 , GLU B:55 , ARG B:56 , VAL B:98 , GLY B:100 , ARG B:101 , VAL B:102 , GLY B:105 , THR B:106 , ASN B:110 , ALA B:111 , GLY B:112 , VAL B:113 , ALA B:215 , VAL B:217 , SER B:256 , ALA B:257 , VAL B:379 , TRP B:458 , HIS B:459 , ASP B:486 , GLY B:487 , HIS B:497 , PRO B:498 , GLN B:499 , TYR B:502 , HOH B:831 , HOH B:841 , HOH B:847 , HOH B:848 , HOH B:851 , HOH B:861 , HOH B:885 , HOH B:976 , HOH B:1058	BINDING SITE FOR RESIDUE FAD B 523
15	BC6	SOFTWARE	NAG B:525 , FUC B:526 , BMA B:527 , HOH B:1432	BINDING SITE FOR RESIDUE NAG B 524
16	BC7	SOFTWARE	LEU B:366 , ASN B:392 , NAG B:524 , FUC B:526 , HOH B:1007 , HOH B:1245	BINDING SITE FOR RESIDUE NAG B 525
17	BC8	SOFTWARE	NAG B:524 , NAG B:525 , HOH B:1277	BINDING SITE FOR RESIDUE FUC B 526
18	BC9	SOFTWARE	ASP A:422 , NAG B:524 , MAN B:528	BINDING SITE FOR RESIDUE BMA B 527
19	CC1	SOFTWARE	LYS A:416 , PRO A:417 , LYS A:419 , ASP A:422 , HOH A:607 , BMA B:527 , HOH B:535 , HOH B:590 , HOH B:625	BINDING SITE FOR RESIDUE MAN B 528
20	CC2	SOFTWARE	ARG B:116 , ASP B:132 , ASN B:135 , ASP B:176 , NAG B:530 , HOH B:866 , HOH B:880 , HOH B:1276 , HOH B:1283 , HOH B:1323	BINDING SITE FOR RESIDUE NAG B 529
21	CC3	SOFTWARE	GLU B:178 , NAG B:529 , BMA B:531 , HOH B:1341 , HOH B:1373	BINDING SITE FOR RESIDUE NAG B 530
22	CC4	SOFTWARE	NAG B:530 , MAN B:532 , HOH B:1291 , HOH B:1380	BINDING SITE FOR RESIDUE BMA B 531
23	CC5	SOFTWARE	HIS B:171 , GLU B:178 , BMA B:531 , HOH B:1097 , HOH B:1370	BINDING SITE FOR RESIDUE MAN B 532
24	CC6	SOFTWARE	ALA A:519 , HOH A:1267 , ASN B:352 , ASN B:430 , HOH B:1232 , HOH B:1502 , HOH B:1597	BINDING SITE FOR RESIDUE NDG B 533
25	CC7	SOFTWARE	ASN B:118 , SER B:120 , HIS B:177 , ASN B:323 , HOH B:911 , HOH B:921	BINDING SITE FOR RESIDUE NAG B 534

Asymmetric Unit

No.	Residues
1	A:399	-	A:450
2	B:399	-	B:450

Asymmetric Unit

No.	Residues
1	His A:168	-	Pro A:169
2	Ala A:225	-	Pro A:226
3	Gly A:364	-	Pro A:365
4	His B:168	-	Pro B:169
5	Ala B:225	-	Pro B:226
6	Gly B:364	-	Pro B:365

(no "SAP(SNP)/Variant" information available for 3GDP)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_1	PS00623	GMC oxidoreductases signature 1.	MDL2_PRUDU	127-150	2	A:100-123 B:100-123
2	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	MDL2_PRUDU	285-299	2	A:258-272 B:258-272

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_1	PS00623	GMC oxidoreductases signature 1.	MDL2_PRUDU	127-150	1	A:100-123 -
2	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	MDL2_PRUDU	285-299	1	A:258-272 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_1	PS00623	GMC oxidoreductases signature 1.	MDL2_PRUDU	127-150	1	- B:100-123
2	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	MDL2_PRUDU	285-299	1	- B:258-272

(no "Exon" information available for 3GDP)

Asymmetric 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:521
 aligned with MDL2_PRUDU | Q945K2 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:521
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547 
           MDL2_PRUDU    28 LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSASYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASD 548
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------3gdpA01 A:9-146,A:192-297,A:367-389,A:457-521  [code=3.50.50.60, no name defined]                                                         ---------------------------------------------3gdpA01 A:9-146,A:192-297,A:367-389,A:457-521  [code=3.50.50.60, no name defined]                         ---------------------------------------------------------------------3gdpA01                -------------------------------------------------------------------3gdpA01 A:9-146,A:192-297,A:367-389,A:457-521                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.eee.hhh..eeeeeeeee....hhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...hhhhhh...ee...............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeee......eeee.ee.........hhhhhhhhh....eeeee..eeeeeeeee...eeeeeeeee.....eeeeeeeeeeeeee.hhhhhhhhhhhhh.eehhhhhhhh.....ee.....eeee..eeeeeee............eeee...eeeeeeee......................eeeeeeee......eeee...........ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee.........hhhhhhhhhhhhhee....ee...................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------GMC_OXRED_1             --------------------------------------------------------------------------------------------------------------------------------------GMC_OXRED_2    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdp A   1 LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASD 521
                                    10        20        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       510       520

Chain B from PDB  Type:PROTEIN  Length:521
 aligned with MDL2_PRUDU | Q945K2 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:521
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547 
           MDL2_PRUDU    28 LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSASYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASD 548
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------3gdpB01 B:9-146,B:192-297,B:367-389,B:457-521  [code=3.50.50.60, no name defined]                                                         ---------------------------------------------3gdpB01 B:9-146,B:192-297,B:367-389,B:457-521  [code=3.50.50.60, no name defined]                         ---------------------------------------------------------------------3gdpB01                -------------------------------------------------------------------3gdpB01 B:9-146,B:192-297,B:367-389,B:457-521                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.eee.hhh..eeeeeeeee....hhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...hhhhhh...ee...............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeee......eeee.ee.........hhhhhhhhh....eeeee..eeeeeee.......eeeeeee.....eeeeeeeeeeeeee.hhhhhhhhhhhhh.eehhhhhhhh.....ee.....eeee..eeeeeee............eeee...eeeeeeee......................eeeeeeee......eeee...........ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee.........hhhhhhhhhhhhhee....ee...................eee.............hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------GMC_OXRED_1             --------------------------------------------------------------------------------------------------------------------------------------GMC_OXRED_2    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdp B   1 LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASD 521
                                    10        20        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       510       520

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 '\|'

(no "SCOP Domain" information available for 3GDP)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Sweet almond (Prunus dulcis) (2)

1a	3gdpA01	A:9-146,A:192-297,A:367-389,A:457-521
1b	3gdpB01	B:9-146,B:192-297,B:367-389,B:457-521

(no "Pfam Domain" information available for 3GDP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MDL2_PRUDU | Q945K2)

molecular function
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046593	mandelonitrile lyase activity	Catalysis of the reaction: mandelonitrile = cyanide + benzaldehyde.
	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.
	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	GO:0050898	nitrile metabolic process	The chemical reactions and pathways involving nitriles, an organic compound containing trivalent nitrogen attached to one carbon atom. The nitriles are named with reference to the acids produced by their decomposition; for example, hydrocyanic acid is formic nitrile, and methyl cyanide is acetic nitrile.
	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IPA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:225 - Pro A:226	[ RasMol ]
		Ala B:225 - Pro B:226	[ RasMol ]
		Gly A:364 - Pro A:365	[ RasMol ]
		Gly B:364 - Pro B:365	[ RasMol ]
		His A:168 - Pro A:169	[ RasMol ]
		His B:168 - Pro B:169	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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	3gdp
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		Orientation in Membranes	:	OPM
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	MDL2_PRUDU \| Q945K2
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	4.1.2.10
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	MDL2_PRUDU \| Q945K2
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UniProtKB/Swiss-Prot
	MDL2_PRUDU \| Q945K2	:	1ju2 3gdn

1ju2	TRICLINIC CRYSTAL FORM
3gdn	COMPLEX WITH BENZALDEHYDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 25)

Sites (25, 25)

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File