3QXU - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   FREE STRUCTURE OF AN ANTI-METHOTREXATE CDR1-3 GRAFT VHH ANTIBODY

Authors :   S. W. Fanning, J. R. Horn

Date :   02 Mar 11 (Deposition) - 06 Jul 11 (Release) - 11 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: B,D  (1x)

Keywords :   Camelid Single Domain Antibody, Heavy Chain Only, Vhh, Antibody, Anti-Hapten Antibody, Cdr, Hapten Binding, Small Molecule Sensing, Ligand Binding, Low Molecular Weight Compound, Methotrexate, Cdr1, Cdr4, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. W. Fanning, J. R. Horn
An Anti-Hapten Camelid Antibody Reveals A Cryptic Binding Site With Significant Energetic Contributions From A Nonhypervariable Loop.
Protein Sci. V. 20 1196 2011
PubMed-ID: 21557375 | Reference-DOI: 10.1002/PRO.648

Molecule 1 - ANTI-METHOTREXATE CDR1-3 GRAFT
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	LLAMA
	Organism Scientific	:	LAMA GLAMA
	Organism Taxid	:	9844

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	FMT	8	Ligand/Ion	FORMIC ACID

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	FMT	3	Ligand/Ion	FORMIC ACID

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	FMT	5	Ligand/Ion	FORMIC ACID

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID

Biological Unit 4 (1, 5)

No.	Name	Count	Type	Full Name
1	FMT	5	Ligand/Ion	FORMIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:54 , GLY A:55 , ASN A:103 , TYR A:104 , HOH A:1059 , FMT A:2001 , GLN C:41 , HOH C:1053	BINDING SITE FOR RESIDUE FMT A 2000
2	AC2	SOFTWARE	ARG A:32 , SER A:33 , HOH A:1058 , HOH A:1103 , HOH A:1106 , FMT A:2000	BINDING SITE FOR RESIDUE FMT A 2001
3	AC3	SOFTWARE	GLN B:126 , HOH B:1043 , VAL C:14 , GLN C:15 , SER C:130 , HOH C:1073	BINDING SITE FOR RESIDUE FMT A 2002
4	AC4	SOFTWARE	ASP B:102 , ASN B:103 , TYR B:104 , HOH B:1046 , FMT B:2004 , GLN D:41 , ARG D:110	BINDING SITE FOR RESIDUE FMT B 2000
5	AC5	SOFTWARE	ARG B:47 , ARG B:110 , TRP B:121 , HOH B:1018 , HOH B:1042	BINDING SITE FOR RESIDUE FMT B 2002
6	AC6	SOFTWARE	SER B:33 , ALA B:35 , SER B:54 , GLY B:55 , TYR B:104 , HOH B:1002 , FMT B:2000	BINDING SITE FOR RESIDUE FMT B 2004
7	AC7	SOFTWARE	ASP C:101 , ASN C:103 , THR C:106 , GLY C:112 , HOH C:1037 , FMT D:2000	BINDING SITE FOR RESIDUE FMT D 2001
8	AC8	SOFTWARE	SER D:111 , HOH D:1068 , FMT D:2001	BINDING SITE FOR RESIDUE FMT D 2000

Asymmetric Unit

No.	Residues
1	A:24	-	A:98
2	B:24	-	B:98
3	C:24	-	C:98
4	D:24	-	D:98

(no "Cis Peptide Bond" information available for 3QXU)

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

(no "PROSITE Motif" information available for 3QXU)

(no "Exon" information available for 3QXU)

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:124
                                                                                                                                                            
               SCOP domains d3qxua_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeee......eeeeee...hhhhheeeeeeee..hhhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxu A   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119

Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d3qxub_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee......eeeeeeee..eeeeeeeee......eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxu B   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22       |34        44        54        64        74        84        94       104       119       129  
                                                      30|                                                                             113|            
                                                       33                                                                              119

Chain C from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3qxuc_ C: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeee......eeeeee...hhhhheeeeeeee.............ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxu C   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119

Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3qxud_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeeee.....eeeeee...hhhhheeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxu D   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119

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: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Llama (Lama glama) [TaxId: 9844] (62)

1a	d3qxua_	A:
1b	d3qxub_	B:
1c	d3qxuc_	C:
1d	d3qxud_	D:

(no "CATH Domain" information available for 3QXU)

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

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3QXU)

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
		FMT	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qxu)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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)

Access by PDB/NDB ID
	3qxu
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 3QXU)

1i3u	THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH THE DYE RR1
2x6m	STRUCTURE OF A SINGLE DOMAIN CAMELID ANTIBODY FRAGMENT IN COMPLEX WITH A C-TERMINAL PEPTIDE OF ALPHA-SYNUCLEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File