3K3Q - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A LLAMA ANTIBODY COMPLEXED WITH THE C. BOTULINUM NEUROTOXIN SEROTYPE A CATALYTIC DOMAIN

Authors :   A. A. Thompson, J. Dong, J. D. Marks, R. C. Stevens

Date :   04 Oct 09 (Deposition) - 23 Feb 10 (Release) - 07 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Llama, Vhh, Antibody, Botulinum, Neurotoxin, Bont, Cell Junction, Cell Membrane, Cytoplasm, Disulfide Bond, Hydrolase, Membrane, Metal-Binding, Metalloprotease, Pharmaceutical, Protease, Secreted, Synapse, Toxin, Transmembrane, Zinc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Dong, A. A. Thompson, Y. Fan, J. Lou, F. Conrad, M. Ho, M. Pires-Alves, B. A. Wilson, R. C. Stevens, J. D. Marks
A Single-Domain Llama Antibody Potently Inhibits The Enzymatic Activity Of Botulinum Neurotoxin By Binding To The Non-Catalytic Alpha-Exosite Binding Region.
J. Mol. Biol. V. 397 1106 2010
PubMed-ID: 20138889 | Reference-DOI: 10.1016/J.JMB.2010.01.070

Molecule 1 - LLAMA AA1 VHH DOMAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LLAMA VHH IMMUNOGLOBULIN
	Organism Scientific	:	LAMA GLAMA
	Organism Taxid	:	9844

Molecule 2 - BOTULINUM NEUROTOXIN TYPE A
	Chains	:	B
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL FRAGMENT OF BONT CATALYTIC DOMAIN (RESIDUES 3-250)
	Gene	:	BOTA, CBO0806, CLC_0862, NEUROTOXIN CATALYTIC DOMAIN
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM A STR. HALL
	Organism Taxid	:	441771
	Synonym	:	BONT/A, BONTOXILYSIN-A, BOTOX, BOTULINUM NEUROTOXIN A LIGHT CHAIN

Molecule 3 - BOTULINUM NEUROTOXIN TYPE A
	Chains	:	C
	EC Number	:	3.4.24.69
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL FRAGMENT OF BONT CATALYTIC DOMAIN (RESIDUES 251-425)
	Gene	:	BOTA, CBO0806, CLC_0862, NEUROTOXIN CATALYTIC DOMAIN
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM A STR. HALL
	Organism Taxid	:	441771
	Synonym	:	BONT/A, BONTOXILYSIN-A, BOTOX, BOTULINUM NEUROTOXIN A LIGHT CHAIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:223 , HIS B:227 , TYR B:250 , GLU C:262	BINDING SITE FOR RESIDUE ZN B 251

Asymmetric Unit

No.	Residues
1	A:25	-	A:110

Asymmetric Unit

No.	Residues
1	Ile A:124	-	Pro A:125

(no "SAP(SNP)/Variant" information available for 3K3Q)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	1	B:220-229

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	2	B:220-229

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	BXA1_CLOBH	220-229	1	B:220-229

(no "Exon" information available for 3K3Q)

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:137
                                                                                                                                                                         
               SCOP domains d3k3qa_ A: automated matches                                                                                                              SCOP domains
               CATH domains 3k3qA00 A:4-140 Immunoglobulins                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee.........hhhhh....eeeeeee.....eeeeeee......eee.hhhh...eeee.....eeeeee........eeeeeeee...hhhhhhhh....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3q A   4 AVQLVDSGGGTLQAGKSLRLSCAISGLAFDGGAMGSEHRLTAGAMGWFRQAPGKDREFVAAISPRTDETYYAESLEGRFSVSRDAAATMVFLQADNVRLDDTASYYCAADEDVTPRVMGVIPHADHWGQGTLVTVSS 140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           BXA1_CLOBH     2 PFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAY 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k3qB00 B:2-250 Metalloproteases ('zincins'), catalytic domain like                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeehhhhh....eeeeeee..eeeeeee...............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeeee.....eeeee..eeeee........eeee................eeee....eeeeee..-----------.eee.hhhhhhhhhhhhhhhhhh........eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3q B   2 QFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEES-----------GKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAY 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       | -       211       221       231       241         
                                                                                                                                                                                                                               199         211

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with BXA1_CLOBH | A5HZZ9 from UniProtKB/Swiss-Prot  Length:1296

    Alignment length:165
                                   262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412     
           BXA1_CLOBH   253 MSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhh..hhhhhhhhhh.............eee.........................hhhhh...hhhhhee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k3q C 253 MSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK 417
                                   262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Llama (Lama glama) [TaxId: 9844] (5)

d3k3qa_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Zincin-like (46)

Homologous Superfamily: Metalloproteases ('zincins'), catalytic domain like (46)

Lama glama. Organism_taxid: 9844. (1)

3k3qB00

B:2-250

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Lama glama. Organism_taxid: 9844. (1)

3k3qA00

A:4-140

(no "Pfam Domain" information available for 3K3Q)

Asymmetric Unit(hide GO term definitions)

Chain B,C (BXA1_CLOBH | A5HZZ9)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051609	inhibition of neurotransmitter uptake	Any process that prevents the activation of the directed movement of a neurotransmitter into a cell.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044164	host cell cytosol	The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0044156	host cell junction	A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0044231	host cell presynaptic membrane	A specialized area of membrane of the host axon terminal that faces the plasma membrane of the host neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many host synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
	GO:0044221	host cell synapse	The junction between a nerve fiber of one host neuron and another host neuron or muscle fiber or glial cell; the site of interneuronal communication.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	3k3q
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(no "Related Entries Specified in the PDB File" available for 3K3Q)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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