3QXV - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY IN COMPLEX WITH METHOTREXATE

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

Date :   02 Mar 11 (Deposition) - 27 Jul 11 (Release) - 11 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (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, 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 CDR1-4 GRAFT VHH
	Chains	:	A, B, C, D, E
	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	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	MTX	5	Ligand/Ion	METHOTREXATE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MTX	1	Ligand/Ion	METHOTREXATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MTX	1	Ligand/Ion	METHOTREXATE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	MTX	1	Ligand/Ion	METHOTREXATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	MTX	1	Ligand/Ion	METHOTREXATE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	MTX	1	Ligand/Ion	METHOTREXATE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:4 , CYS A:24 , ALA A:26 , ARG A:28 , ARG A:29 , SER A:30 , SER A:31 , TRP A:34 , MET A:36 , ARG A:74 , ASP A:75 , ASN A:76 , TYR A:79 , LEU A:80 , VAL A:81 , ALA A:100 , HOH A:1009	BINDING SITE FOR RESIDUE MTX A 2000
2	AC2	SOFTWARE	GLN A:41 , ARG A:47 , ARG A:110	BINDING SITE FOR RESIDUE SO4 A 3000
3	AC3	SOFTWARE	GLU B:46 , ARG B:47	BINDING SITE FOR RESIDUE SO4 B 3000
4	AC4	SOFTWARE	SER B:33 , ALA B:35 , SER B:54 , GLY B:55 , ASP B:102	BINDING SITE FOR RESIDUE SO4 B 3001
5	AC5	SOFTWARE	VAL B:4 , CYS B:24 , ALA B:26 , ARG B:28 , SER B:30 , SER B:31 , TRP B:34 , ARG B:74 , ASP B:75 , ASN B:76 , TYR B:79 , LEU B:80 , VAL B:81 , ALA B:100 , TYR B:120	BINDING SITE FOR RESIDUE MTX B 2000
6	AC6	SOFTWARE	CYS C:24 , ALA C:26 , ARG C:28 , SER C:30 , MET C:36 , ARG C:74 , ASP C:75 , ASN C:76 , TYR C:79 , LEU C:80 , VAL C:81 , ALA C:100	BINDING SITE FOR RESIDUE MTX C 2000
7	AC7	SOFTWARE	GLN C:41 , ARG C:47 , ARG C:110	BINDING SITE FOR RESIDUE SO4 C 3000
8	AC8	SOFTWARE	VAL D:4 , CYS D:24 , ALA D:26 , ARG D:28 , SER D:30 , SER D:31 , TRP D:34 , ARG D:74 , ASP D:75 , ASN D:76 , TYR D:79 , LEU D:80 , VAL D:81 , ALA D:100 , TYR D:120 , HOH D:1003	BINDING SITE FOR RESIDUE MTX D 2000
9	AC9	SOFTWARE	GLY D:44 , CYS E:24 , ALA E:26 , ARG E:28 , SER E:30 , SER E:31 , TRP E:34 , MET E:36 , ARG E:74 , ASP E:75 , ASN E:76 , TYR E:79 , LEU E:80 , VAL E:81 , ALA E:100	BINDING SITE FOR RESIDUE MTX E 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
5	E:24	-	E:98

Asymmetric Unit

No.	Residues
1	Ala E:16	-	Gly E:17
2	Gly E:17	-	Gly E:18

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

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

(no "Exon" information available for 3QXV)

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:123
                                                                                                                                                           
               SCOP domains d3qxva_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee........eeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxv A   4 VQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDNAEYLVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    13        23        33        43        53        63        73        83        93       103       113|      128   
                                                                                                                                       113|            
                                                                                                                                        119

Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d3qxvb_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee..hhhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxv B   4 VQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDNAEYLVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    13        23        33        43        53        63        73        83        93       103       113|      128   
                                                                                                                                       113|            
                                                                                                                                        119

Chain C from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d3qxvc_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeee........eeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxv C   4 VQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDNAEYLVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    13        23        33        43        53        63        73        83        93       103       113|      128   
                                                                                                                                       113|            
                                                                                                                                        119

Chain D from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3qxvd_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee........eeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...hhhhh.....ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxv D   3 QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAKISGDGRLTTYGDSVKGRFTISRDNAEYLVYLQMDSLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTVSS 131
                                    12        22        32        42        52        62        72        82        92       102       112||     127    
                                                                                                                                        113|            
                                                                                                                                         119

Chain E from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d3qxve_ E: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeeeeee........eeeeee....eeeeee......eee.hhhh..eeeeee....eeeeee..hhhhheeeeeeee.............ee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3qxv E   4 VQLVESGQAGGSLRLSCAASRRSSRSWAMAWFRAKEREFVAKISGDGRLTTYGDSVKGRFTISRDNAEYLVYLQMDLKPEDTAVYYCAADDNYVTASWRSGPDYWGQGTQVTV 129
                                  ||17        27        37  |||   50        60        70        80     || 91       101       111 ||    126   
                                 10|                       40||                                       86|                      113|          
                                  15                        42|                                        88                       119          
                                                             45

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	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

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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	d3qxva_	A:
1b	d3qxvd_	D:
1c	d3qxve_	E:
1d	d3qxvb_	B:
1e	d3qxvc_	C:

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

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

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	Cis Peptide Bonds
		Ala E:16 - Gly E:17	[ RasMol ]
		Gly E:17 - Gly E:18	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

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