1KXV - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CAMELID VHH DOMAINS IN COMPLEX WITH PORCINE PANCREATIC ALPHA-AMYLASE

Authors :   A. Desmyter, S. Spinelli, F. Payan, M. Lauwereys, L. Wyns, S. Muyldermans, C. Cambillau

Date :   01 Feb 02 (Deposition) - 19 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Beta 8 Alpha 8, Beta Barrel, Hydrolase, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Desmyter, S. Spinelli, F. Payan, M. Lauwereys, L. Wyns, S. Muyldermans, C. Cambillau
Three Camelid Vhh Domains In Complex With Porcine Pancreatic Alpha-Amylase. Inhibition And Versatility Of Binding Topology.
J. Biol. Chem. V. 277 23645 2002
PubMed-ID: 11960990 | Reference-DOI: 10.1074/JBC.M202327200
(for further references see the PDB file header)

Molecule 1 - ALPHA-AMYLASE, PANCREATIC
	Chains	:	A, B
	EC Number	:	3.2.1.1
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Other Details	:	PANCEATIC ENZYME
	Synonym	:	1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE

Molecule 2 - CAMELID VHH DOMAIN CAB10
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHEN6
	Expression System Strain	:	WK
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	ARABIAN CAMEL
	Organism Scientific	:	CAMELUS DROMEDARIUS
	Organism Taxid	:	9838

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1KXV)

(no "Site" information available for 1KXV)

Asymmetric Unit

No.	Residues
1	A:28	-	A:86
2	A:70	-	A:115
3	A:141	-	A:160
4	A:378	-	A:384
5	A:450	-	A:462
6	B:28	-	B:86
7	B:70	-	B:115
8	B:141	-	B:160
9	B:378	-	B:384
10	B:450	-	B:462
11	C:22	-	C:95
12	C:30	-	C:106
13	D:22	-	D:95
14	D:30	-	D:106

Asymmetric Unit

No.	Residues
1	Asn A:53	-	Pro A:54
2	Val A:129	-	Pro A:130
3	Asn B:53	-	Pro B:54
4	Val B:129	-	Pro B:130

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

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

(no "Exon" information available for 1KXV)

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:496
 aligned with AMYP_PIG | P00690 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:496
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      
             AMYP_PIG    16 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGQDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWRQIRNMVWFRNVVDGQPFANWWANGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1kxva2 A:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1kxva1 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains 1kxvA01 A:1-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                       1kxvA02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhh...eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee........ee..ee................hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kxv A   1 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGSREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIKSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGSSILTFWDARLYKIAVGFMLAHPYGFTRVMSSYRWARNFVNGEDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWREIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 496
                                    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

Chain B from PDB  Type:PROTEIN  Length:496
 aligned with AMYP_PIG | P00690 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:496
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      
             AMYP_PIG    16 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGQDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWRQIRNMVWFRNVVDGQPFANWWANGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1kxvb2 B:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1kxvb1 B:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains 1kxvB01 B:1-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                       1kxvB02 B:404-496 Golgi alpha-mannosidase II                                                  CATH domains
           Pfam domains (1) ---------------------Alpha-amylase-1kxvB03 B:22-336                                                                                                                                                                                                                                                                                             ------------------------------------------------------------------------Alpha-amylase_C-1kxvB01 B:409-495                                                      - Pfam domains (1)
           Pfam domains (2) ---------------------Alpha-amylase-1kxvB04 B:22-336                                                                                                                                                                                                                                                                                             ------------------------------------------------------------------------Alpha-amylase_C-1kxvB02 B:409-495                                                      - Pfam domains (2)
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh...............eeee..........hhhhhh...eee.hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee........ee..ee................hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...eeeeee.....eeeeee.....eeee...............eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kxv B   1 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGSREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIKSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGSSILTFWDARLYKIAVGFMLAHPYGFTRVMSSYRWARNFVNGEDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWREIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 496
                                    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

Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d1kxvc_ C: Camelid IG heavy chain variable domain, VHh                                                                  SCOP domains
               CATH domains 1kxvC00 C:2-120 Immunoglobulins                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee......eeeeeeee.....eeeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeeee...............eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1kxv C   2 VQLVESGGGTVPAGGSLRLSCAASGNTLCTYDMSWYRRAPGKGRDFVSGIDNDGTTTYVDSVAGRFTISQGNAKNTAYLQMDSLKPDDTAMYYCKPSLRYGLPGCPIIPWGQGTQVTVS 120
                                    11        21        31        41        51        61        71        81        91       101       111

Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d1kxvd_ D: Camelid IG heavy chain variable domain, VHh                                                                    SCOP domains
               CATH domains 1kxvD00 D:1-121 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee......eeeeeeee.....eeeeeee.....eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeeee...............eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kxv D   1 QVQLVESGGGTVPAGGSLRLSCAASGNTLCTYDMSWYRRAPGKGRDFVSGIDNDGTTTYVDSVAGRFTISQGNAKNTAYLQMDSLKPDDTAMYYCKPSLRYGLPGCPIIPWGQGTQVTVSS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Pig (Sus scrofa) (20)

1a	1kxvA01	A:1-403
1b	1kxvB01	B:1-403

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Golgi alpha-mannosidase II (346)

Pig (Sus scrofa) (16)

2a	1kxvA02	A:404-496
2b	1kxvB02	B:404-496

Homologous Superfamily: Immunoglobulins (2282)

Pig (Sus scrofa) (3)

3a	1kxvC00	C:2-120
3b	1kxvD00	D:1-121

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GHD (106)

Family: Alpha-amylase_C (82)

Sus scrofa (Pig) (13)

1a	Alpha-amylase_C-1kxvB01	B:409-495
1b	Alpha-amylase_C-1kxvB02	B:409-495

Clan: Glyco_hydro_tim (488)

Family: Alpha-amylase (138)

Sus scrofa (Pig) (13)

2a	Alpha-amylase-1kxvB03	B:22-336
2b	Alpha-amylase-1kxvB04	B:22-336

Asymmetric Unit(hide GO term definitions)

Chain A,B (AMYP_PIG | P00690)

molecular function
	GO:0004556	alpha-amylase activity	Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0043169	cation binding	Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
	GO:0031404	chloride ion binding	Interacting selectively and non-covalently with chloride ions (Cl-).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0016052	carbohydrate catabolic process	The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asn A:53 - Pro A:54	[ RasMol ]
		Asn B:53 - Pro B:54	[ RasMol ]
		Val A:129 - Pro A:130	[ RasMol ]
		Val B:129 - Pro B:130	[ RasMol ]

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	1kxv
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1kxq	CAMELID VHH DOMAIN IN COMPLEX WITH PORCINE PANCREATIC ALPHA -AMYLASE
1kxt	CAMELID VHH DOMAINS IN COMPLEX WITH PORCINE PANCREATIC ALPHA-AMYLASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (14, 14)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (3, 6)

CATH Domains (3, 6)

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