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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 3E5 IGG3 FAB FROM MUS MUSCULUS

Authors :   A. Janda, E. Eryilmaz, J. Kim, R. J. B. Cordero, D. Cowburn, A. Casadeval

Date :   02 Oct 12 (Deposition) - 17 Apr 13 (Release) - 21 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Igg, Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Eryilmaz, A. Janda, J. Kim, R. J. Cordero, D. Cowburn, A. Casadevall
Global Structures Of Igg Isotypes Expressing Identical Variable Regions.
Mol. Immunol. V. 56 588 2013
PubMed-ID: 23911417 | Reference-DOI: 10.1016/J.MOLIMM.2013.06.006

Molecule 1 - KAPPA LIGHT CHAIN VARIABLE REGION, ANTI-COLORECTAL CARCINOMA LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Gene	:	IGG1 ANTI-TS1 VL, GM16939
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IG HEAVY CHAIN V REGION RF, IG GAMMA-3 CHAIN C REGION
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:			H	L
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4HDI)

(no "Site" information available for 4HDI)

Asymmetric Unit

No.	Residues
1	A:23	-	A:93
2	A:139	-	A:199
3	B:22	-	B:96
4	B:147	-	B:202
5	H:22	-	H:96
6	H:147	-	H:202
7	L:23	-	L:93
8	L:139	-	L:199
9	L:219	-	H:135

Asymmetric Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Val L:99	-	Pro L:100
3	Tyr L:145	-	Pro L:146
4	Phe H:153	-	Pro H:154
5	Glu H:155	-	Pro H:156
6	Trp H:195	-	Pro H:196
7	Thr A:7	-	Pro A:8
8	Val A:99	-	Pro A:100
9	Tyr A:145	-	Pro A:146
10	Phe B:153	-	Pro B:154
11	Glu B:155	-	Pro B:156
12	Trp B:195	-	Pro B:196

(no "SAP(SNP)/Variant" information available for 4HDI)

(no "PROSITE Motif" information available for 4HDI)

(no "Exon" information available for 4HDI)

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:217
                                                                                                                                                                                                                                                         
               SCOP domains d4hdia1 A:1-112 automated matches                                                                               d4hdia2 A:113-217 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...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
                 4hdi A   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVANRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.hhhhh...eeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdi B   2 VKLVESGGGLVKLGGSLKLSCAASGFTFSNYFMSWVRQTPEKRLELVAVITSNGDNTYYPDTVKGRFTISRDNAQNTLYLQMSSLKSEDTALYYCARRDSSASLYFDYWGQGTTLTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeehhhhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdi H   1 DVKLVESGGGLVKLGGSLKLSCAASGFTFSNYFMSWVRQTPEKRLELVAVITSNGDNTYYPDTVKGRFTISRDNAQNTLYLQMSSLKSEDTALYYCARRDSSASLYFDYWGQGTTLTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d4hdil1 L:1-112 automated matches                                                                               d4hdil2 L:113-219 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdi L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVANRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

1a	d4hdia2	A:113-217
1b	d4hdil2	L:113-219

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

Protein domain: automated matches (311)

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

2a	d4hdia1	A:1-112
2b	d4hdil1	L:1-112

(no "CATH Domain" information available for 4HDI)

(no "Pfam Domain" information available for 4HDI)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4hdi)

	Sites
(no "Sites" information available for 4hdi)

	Cis Peptide Bonds
		Glu B:155 - Pro B:156	[ RasMol ]
		Glu H:155 - Pro H:156	[ RasMol ]
		Phe B:153 - Pro B:154	[ RasMol ]
		Phe H:153 - Pro H:154	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp B:195 - Pro B:196	[ RasMol ]
		Trp H:195 - Pro H:196	[ RasMol ]
		Tyr A:145 - Pro A:146	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]
		Val A:99 - Pro A:100	[ RasMol ]
		Val L:99 - Pro L:100	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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(no "Related Entries Specified in the PDB File" available for 4HDI)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (9, 9)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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