1PZ5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL BASIS OF PEPTIDE-CARBOHYDRATE MIMICRY IN AN ANTIBODY COMBINING SITE

Authors :   N. K. Vyas, M. N. Vyas, M. C. Chervenak, D. R. Bundle, B. M. Pinto, F. A. Qui

Date :   09 Jul 03 (Deposition) - 18 Nov 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Antibody-Antigen Structure, Peptide-Carbohydrate Mimicry, Vaccine Design, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Vyas, M. N. Vyas, M. C. Chervenak, D. R. Bundle, B. M. Pinto, F. A. Quiocho
Structural Basis Of Peptide-Carbohydrate Mimicry In An Antibody Combining Site.
Proc. Natl. Acad. Sci. Usa V. 100 15023 2003
PubMed-ID: 14645714 | Reference-DOI: 10.1073/PNAS.2431286100
(for further references see the PDB file header)

Molecule 1 - LIGHT CHAIN OF FAB (SYA/J6)
	Chains	:	A
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - HEAVY CHAIN OF FAB (SYA/J6)
	Chains	:	B
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 3 - OCTAPEPTIDE (MDWNMHAA)
	Chains	:	C
	Engineered	:	YES
	Other Details	:	THE OCTAPEPTIDE WAS SYNTHESIZED AS ITS CARBOXAMIDE (ALBERTA PEPTIDE INSTITURE, EDMONTON, CANADA)
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1PZ5)

(no "Site" information available for 1PZ5)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195

Asymmetric/Biological Unit

No.	Residues
1	Thr A:7	-	Pro A:8
2	Tyr A:140	-	Pro A:141
3	Phe B:146	-	Pro B:147
4	Glu B:148	-	Pro B:149
5	Trp B:188	-	Pro B:189

(no "SAP(SNP)/Variant" information available for 1PZ5)

(no "PROSITE Motif" information available for 1PZ5)

(no "Exon" information available for 1PZ5)

Asymmetric/Biological 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:215
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  216
               SCOP domains d1pz5a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1pz5a2 A:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1pz5A01 A:1-108 Immunoglobulins                                                                                  -1pz5A02 A:110-209 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....-ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1pz5 A    1 DVVLTQTPLSLPVRLGDQASISCRSSQSLLHSDGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQTTHVP-TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C||      35        45        55        65        75        85        95 |     105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                  95 |                                                                                                                  
                                                      27B|||                                                                    97                                                                                                                  
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with HVM32_MOUSE | P01801 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:220
                                                                                                                              101   102          115                                                                                                    
                                    10        20        30        40        50        60        70        80        90       100|     |105       115         -         -         -         -         -         -         -         -         -         -
         HVM32_MOUSE      1 EVKLEESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTTG-----FAYWGQGTLVTVSA----------------------------------------------------------------------------------------------------    -
               SCOP domains d1pz5b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1pz5b2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1pz5B01 B:1-113 Immunoglobulins                                                                                         1pz5B02 B:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pz5 B    1 EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTRGGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKVDLIKEISGP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |103       113       123       133       143       153       163       173       183       193       203       213
                                                                              52A||                            82A||               100A                                                                                                                 
                                                                               52B|                             82B|                                                                                                                                    
                                                                                52C                              82C

Chain C from PDB  Type:PROTEIN  Length:8
                                         
               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
                1pz5 C    1 MDWNMHAA    8

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1pz5A02	A:110-209
1b	1pz5B02	B:114-212
1c	1pz5A01	A:1-108
1d	1pz5B01	B:1-113

(no "Pfam Domain" information available for 1PZ5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A2NHM3_MOUSE | A2NHM3)

Chain B (HVM32_MOUSE | P01801)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pz5)

	Sites
(no "Sites" information available for 1pz5)

	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Trp B:188 - Pro B:189	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]

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	1pz5
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1m71	UNLIGANDED FORM OF THE FAB
1m7d	OLIGOSACCHARIDE BOUND FORM OF THE FAB
1m7i	OLIGOSACCHARIDE BOUND FORM OF THE FAB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 4)

CATH Domains (1, 4)

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Gene Ontology (1, 1)

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