3IF1 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 237MAB IN COMPLEX WITH A GALNAC

Authors :   C. L. Brooks, S. V. Evans, S. N. Borisova

Date :   23 Jul 09 (Deposition) - 23 Jun 10 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Glycopepitde, Antibody, Fab, Carbohydrate-Biding, Tumour, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Brooks, A. Schietinger, S. N. Borisova, P. Kufer, M. Okon, T. Hirama, C. R. Mackenzie, L. X. Wang, H. Schreiber, S. V. Evans
Antibody Recognition Of A Unique Tumor-Specific Glycopeptid Antigen.
Proc. Natl. Acad. Sci. Usa V. 107 10056 2010
PubMed-ID: 20479270 | Reference-DOI: 10.1073/PNAS.0915176107
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN (IGG2A)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN (IGG2A)
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	MG	5	Ligand/Ion	MAGNESIUM ION
2	NGA	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
3	ZN	5	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NGA	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:34 , HOH A:218 , HOH A:229 , HOH B:225	BINDING SITE FOR RESIDUE ZN A 213
02	AC2	SOFTWARE	GLU A:185 , HIS A:189 , HOH A:216 , HOH A:259	BINDING SITE FOR RESIDUE ZN A 215
03	AC3	SOFTWARE	ILE A:2 , GLN A:3 , ASP A:60 , MG A:214 , HOH A:243	BINDING SITE FOR RESIDUE ZN A 222
04	AC4	SOFTWARE	ASN A:138 , ASP A:167 , ASP A:170 , HIS B:164	BINDING SITE FOR RESIDUE MG A 1
05	AC5	SOFTWARE	GLN A:3 , ASP A:60 , ZN A:222 , HOH A:234	BINDING SITE FOR RESIDUE MG A 214
06	AC6	SOFTWARE	HIS A:27D , TYR A:32 , SER A:91 , THR A:92 , HIS A:93 , TRP B:33 , TRP B:47 , GLU B:50 , ARG B:52 , TYR B:58 , ARG B:98 , HOH B:248	BINDING SITE FOR RESIDUE NGA B 1A
07	AC7	SOFTWARE	HIS B:55 , GLU C:123 , HOH C:221 , HOH C:238	BINDING SITE FOR RESIDUE ZN C 218
08	AC8	SOFTWARE	ILE C:2 , GLN C:27 , ASP C:60 , MG C:213	BINDING SITE FOR RESIDUE MG C 1
09	AC9	SOFTWARE	MG C:1 , GLN C:3 , ASP C:60	BINDING SITE FOR RESIDUE MG C 213
10	BC1	SOFTWARE	HIS C:34 , HOH C:215 , HOH C:235	BINDING SITE FOR RESIDUE MG C 214
11	BC2	SOFTWARE	ASP A:143 , HOH A:240 , HIS D:55	BINDING SITE FOR RESIDUE ZN D 221
12	BC3	SOFTWARE	HIS C:27D , TYR C:32 , SER C:91 , THR C:92 , HIS C:93 , GLU D:50 , ARG D:52 , TYR D:58 , ARG D:98 , HOH D:421	BINDING SITE FOR RESIDUE NGA D 213

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:92
8	D:140	-	D:195

Asymmetric Unit

No.	Residues
1	Ser 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
6	Ser C:7	-	Pro C:8
7	Tyr C:140	-	Pro C:141
8	Phe D:146	-	Pro D:147
9	Glu D:148	-	Pro D:149
10	Trp D:188	-	Pro D:189

(no "SAP(SNP)/Variant" information available for 3IF1)

(no "PROSITE Motif" information available for 3IF1)

(no "Exon" information available for 3IF1)

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:215
                                                                                                                                                                                                                                                       
               SCOP domains d3if1a1 A:2-112 automated matches                                                                                  d3if1a2 A:113-212 automated matches                                                                  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..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3if1 A   2 IQLTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISSVEAEDLGVYFCSQSTHVPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRE 212
                                    11        21      |27D|       36        46        56        66        76        86        97       107       117       127       137       147       157       167       177       187       197       207     
                                                    27A||||                                                                  95|                                                                                                                   
                                                     27B|||                                                                   97                                                                                                                   
                                                      27C||                                                                                                                                                                                        
                                                       27D|                                                                                                                                                                                        
                                                        27E

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee........eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....ee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3if1 B   1 QVQLQQSGGGLVQPGGSMKIFCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHETYYAESVKGRFTITRDDSKSRMSLQMNSLRAEDTGIYYCSGGKVRNAYWGQGTTVTVSSKTTKAPSVYPLAPVSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP 212
                                    10        20        30        40        50  |||   57        67        77     |||84        94     ||105       115       125 ||    142       152       162       172       182       192       202       212
                                                                              52A||                            82A||               100|                      127|                                                                             
                                                                               52B|                             82B|                102                       135                                                                             
                                                                                52C                              82C

Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d3if1c1 C:2-112 automated matches                                                                                  d3if1c2 C:113-212 automated matches                                                                  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..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3if1 C   2 IQLTQSPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISSVEAEDLGVYFCSQSTHVPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRE 212
                                    11        21      |27D|       36        46        56        66        76        86        97       107       117       127       137       147       157       167       177       187       197       207     
                                                    27A||||                                                                  95|                                                                                                                   
                                                     27B|||                                                                   97                                                                                                                   
                                                      27C||                                                                                                                                                                                        
                                                       27D|                                                                                                                                                                                        
                                                        27E

Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee........eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....ee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3if1 D   1 QVQLQQSGGGLVQPGGSMKIFCAASGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHETYYAESVKGRFTITRDDSKSRMSLQMNSLRAEDTGIYYCSGGKVRNAYWGQGTTVTVSSKTTKAPSVYPLAPVSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP 212
                                    10        20        30        40        50  |||   57        67        77     |||84        94     ||105       115       125 ||    142       152       162       172       182       192       202       212
                                                                              52A||                            82A||               100|                      127|                                                                             
                                                                               52B|                             82B|                102                       135                                                                             
                                                                                52C                              82C

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)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d3if1a2	A:113-212
1b	d3if1c2	C:113-212

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

Protein domain: automated matches (311)

Mouse (Mus musculus) [TaxId: 10090] (112)

2a	d3if1a1	A:2-112
2b	d3if1c1	C:2-112

(no "CATH Domain" information available for 3IF1)

(no "Pfam Domain" information available for 3IF1)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3IF1)

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

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3iet	CRYSTAL STRUCTURE OF 237MAB WITH ANTIGEN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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