3QG6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR LIGAND RECOGNITION AND DISCRIMINATION OF A QUORUM QUENCHING ANTIBODY

Authors :   R. N. Kirchdoerfer, J. D. Janda, G. F Kaufmann, I. A Wilson

Date :   24 Jan 11 (Deposition) - 23 Mar 11 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Immunoglobulin Fold, Antigen Binding, Aip4 Binding, Secreted, Immune System-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. N. Kirchdoerfer, A. L. Garner, C. E. Flack, J. M. Mee, A. R. Horswill, K. D. Janda, G. F. Kaufmann, I. A. Wilson
Structural Basis For Ligand Recognition And Discrimination Of A Quorum-Quenching Antibody.
J. Biol. Chem. V. 286 17351 2011
PubMed-ID: 21454495 | Reference-DOI: 10.1074/JBC.M111.231258

Molecule 1 - AP4-24H11 LIGHT CHAIN
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	HYBRIDOMA
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - AP4-24H11 HEAVY CHAIN
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	HYBRIDOMA
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - AGR AUTOINDUCING PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	H	L
Biological Unit 1 (1x)	:	A	B		D
Biological Unit 2 (1x)	:			C		H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	ZN	9	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:1 , HOH A:247 , GLU L:213	BINDING SITE FOR RESIDUE ZN A 214
02	AC2	SOFTWARE	GLU A:185 , HIS A:189 , GLU H:85 , HOH H:292	BINDING SITE FOR RESIDUE ZN A 216
03	AC3	SOFTWARE	HIS A:93 , HOH A:271	BINDING SITE FOR RESIDUE ZN A 217
04	AC4	SOFTWARE	ASP B:72 , SER B:74	BINDING SITE FOR RESIDUE ZN B 229
05	AC5	SOFTWARE	HIS H:82A	BINDING SITE FOR RESIDUE ZN H 229
06	AC6	SOFTWARE	GLU B:85 , HOH B:291 , GLU L:185 , HIS L:189	BINDING SITE FOR RESIDUE ZN L 215
07	AC7	SOFTWARE	HIS L:93 , HOH L:232 , HOH L:278 , HOH L:279	BINDING SITE FOR RESIDUE ZN L 216
08	AC8	SOFTWARE	ASP L:60 , HOH L:251	BINDING SITE FOR RESIDUE ZN L 217
09	AC9	SOFTWARE	GLU A:213 , ASP L:1 , HOH L:277	BINDING SITE FOR RESIDUE ZN L 218
10	BC1	SOFTWARE	GLY B:164 , HOH C:277 , ASN H:32 , TYR H:33 , ALA H:34 , ASN H:35A , PHE H:50 , TYR H:54 , GLU H:95 , TYR L:32 , HIS L:34 , TYR L:49 , THR L:91 , TYR L:96 , HOH L:248	BINDING SITE FOR CHAIN C OF AGR AUTOINDUCING PEPTIDE
11	BC2	SOFTWARE	TYR A:32 , HIS A:34 , THR A:91 , TYR A:96 , ASN B:32 , TYR B:33 , ALA B:34 , ASN B:35A , PHE B:50 , SER B:52 , GLU B:95 , GLY B:96 , HOH D:136	BINDING SITE FOR CHAIN D OF AGR AUTOINDUCING PEPTIDE

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:208
5	H:22	-	H:92
6	H:142	-	H:208
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Thr A:7	-	Pro A:8
2	Val A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:148	-	Pro B:149
5	Glu B:150	-	Pro B:151
6	Trp B:199	-	Pro B:200
7	Phe H:148	-	Pro H:149
8	Glu H:150	-	Pro H:151
9	Trp H:199	-	Pro H:200
10	Thr L:7	-	Pro L:8
11	Val L:94	-	Pro L:95
12	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 3QG6)

(no "PROSITE Motif" information available for 3QG6)

(no "Exon" information available for 3QG6)

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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg6 A   1 DVVLTQTPLSLPVSLGDQASISCRSSQRLVHSNGNIYLHWFLQKPGQSPKLLIYKLSSRFSGVPDRFSGSGSGTDFTLKISRVESEDLGIYYCSQTTHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeee.....eeeeeee.....eee......eeeeeeehhh.eeeeeee..hhhhheeeeee.........eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg6 B   1 DVQLQESGPGLVKPSQSLSLTCTVTGYSITSNYAWNWIRQFPGNKLEWMGFISSYGTTTYNPSLKSRFSITRDTSKNQFFLQLHSVTIEDTGTYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPS 228
                                    10        20        30     |  39        49        59        69        79   |||  86        96|      110       120       136       146       157|      172       184       194 || || 206|      217     ||  
                                                             35A                                             82A||            96|                        128|                154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|            101                         135                 156||     171       183           198 ||  208             226  
                                                                                                               82C                                                             157|                               200|                       
                                                                                                                                                                                162                                202

Chain C from PDB  Type:PROTEIN  Length:6
 aligned with Q9F6Z3_STAAU | Q9F6Z3 from UniProtKB/TrEMBL  Length:46

    Alignment length:6
         Q9F6Z3_STAAU    27 TCYFIM  32
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3qg6 C   3 TCYFIM   8

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with Q9F6Z3_STAAU | Q9F6Z3 from UniProtKB/TrEMBL  Length:46

    Alignment length:7
         Q9F6Z3_STAAU    26 STCYFIM  32
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3qg6 D   2 STCYFIM   8

Chain H from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeee.....eeeeeee.....eee......eeeeeee....eeeeeee..hhhhheeeeee.........eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg6 H   1 DVQLQESGPGLVKPSQSLSLTCTVTGYSITSNYAWNWIRQFPGNKLEWMGFISSYGTTTYNPSLKSRFSITRDTSKNQFFLQLHSVTIEDTGTYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP 227
                                    10        20        30     |  39        49        59        69        79   |||  86        96|      110       120       136       146       157|      172       184       194 || || 206|      217     || 
                                                             35A                                             82A||            96|                        128|                154|||    169|      180|          196| || 206|            223| 
                                                                                                              82B|            101                         135                 156||     171       183           198 ||  208             226 
                                                                                                               82C                                                             157|                               200|                      
                                                                                                                                                                                162                                202

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg6 L   1 DVVLTQTPLSLPVSLGDQASISCRSSQRLVHSNGNIYLHWFLQKPGQSPKLLIYKLSSRFSGVPDRFSGSGSGTDFTLKISRVESEDLGIYYCSQTTHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "SCOP Domain" information available for 3QG6)

(no "CATH Domain" information available for 3QG6)

(no "Pfam Domain" information available for 3QG6)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3QG6)

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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Glu B:150 - Pro B:151	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp B:199 - Pro B:200	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val A:94 - Pro A:95	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

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	3qg6
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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