3DUU - JenaLib

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Title :   CRYSTAL STRUCTURE OF SAG506-01, ORTHORHOMBIC, TWINNED, CRYSTAL 2

Authors :   C. L. Brooks, R. J. Blackler, S. Gerstenbruch, P. Kosma, S. Muller- Loennies, H. Brade, S. V. Evans

Date :   17 Jul 08 (Deposition) - 02 Dec 08 (Release) - 02 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Antibody, Kdo, Twinning, Pseudo-Symmetry, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Brooks, R. J. Blackler, S. Gerstenbruch, P. Kosma, S. Muller-Loennies, H. Brade, S. V. Evans
Pseudo-Symmetry And Twinning In Crystals Of Homologous Antibody Fv Fragments.
Acta Crystallogr. , Sect. D V. 64 1250 2008
PubMed-ID: 19018101 | Reference-DOI: 10.1107/S0907444908033453
(for further references see the PDB file header)

Molecule 1 - ANTIBODY FV FRAGMENT SAG506-01
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSFJ8
	Expression System Strain	:	TG1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	VARIABLE REGION FRAGMENT (FV)
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IG-LIKE PROTEIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	KDO	2	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	KDO	1	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	KDO	1	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:27D , SER A:91 , TYR A:92 , ARG A:95 , HOH A:121 , TYR B:33 , PHE B:50 , ARG B:52 , ASP B:100	BINDING SITE FOR RESIDUE KDO B 114
2	AC2	SOFTWARE	LYS C:27D , TYR C:32 , SER C:91 , TYR C:92 , ARG C:95 , TYR D:33 , PHE D:50 , ARG D:52 , GLY D:96 , ASP D:100 , HOH D:122	BINDING SITE FOR RESIDUE KDO D 114
3	AC3	SOFTWARE	HOH A:151 , HOH B:132 , GLN C:79 , HOH C:117 , HOH C:126	BINDING SITE FOR RESIDUE MG C 111
4	AC4	SOFTWARE	HOH A:128 , GLU C:55 , HOH C:122 , HOH C:152	BINDING SITE FOR RESIDUE MG A 112
5	AC5	SOFTWARE	GLN A:79 , HOH A:128 , HOH C:122 , HOH D:154	BINDING SITE FOR RESIDUE MG C 113
6	AC6	SOFTWARE	LYS B:53 , HOH B:142 , PRO C:40 , GLY C:41	BINDING SITE FOR RESIDUE PG4 B 115
7	AC7	SOFTWARE	GLY A:41 , LYS D:53 , TYR D:97	BINDING SITE FOR RESIDUE PG4 D 115

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	B:22	-	B:92
3	C:23	-	C:88
4	D:22	-	D:92

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Ser C:7	-	Pro C:8

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

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

(no "Exon" information available for 3DUU)

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:112
 aligned with A0N262_MOUSE | A0N262 from UniProtKB/TrEMBL  Length:115

    Alignment length:112
                                                                                                                            98              
                                                                                                                          97 |              
                                    11        21        31        41        51        61        71        81        91     | 100       110  
        A0N262_MOUSE      2 DIQLTQSPSSLAVSAGEKVTMSCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCHQ-YLSHTFGGGTKLEIK  112
               SCOP domains d3duua_ A: automated matches                                                                                     SCOP domains
               CATH domains 3duuA00 A:1-106 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee....eeeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee.....ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                3duu A    1 DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYNLRTFGGGTKLELK  106
                                    10        20       27C|||     34        44        54        64        74        84        94       104  
                                                     27A|||||                                                                               
                                                      27B||||                                                                               
                                                       27C|||                                                                               
                                                        27D||                                                                               
                                                         27E|                                                                               
                                                          27F

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with A2NU21_MOUSE | A2NU21 from UniProtKB/TrEMBL  Length:119

    Alignment length:121
                                                                                                                              119                    
                                    28        38        48        58        68        78        88        98       108       118|        -         - 
        A2NU21_MOUSE     19 EVKLVESGGGLVQPGGSLSLSCAASGFTFTDYYMSWVRQLPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCAKD--------------------    -
               SCOP domains d3duub_ B: automated matches                                                                                              SCOP domains
               CATH domains 3duuB00 B:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee..hhhhheeeeeee......eeeeee........eee.......eeeeee....eeeeeee........eeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3duu B    1 EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTVEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDGYYVDAMDYWGQGTSVTVSS  113
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |102       112 
                                                                              52A||                            82A||               100A|             
                                                                               52B|                             82B|                100B             
                                                                                52C                              82C

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with A0N262_MOUSE | A0N262 from UniProtKB/TrEMBL  Length:115

    Alignment length:112
                                                                                                                            98              
                                                                                                                          97 |              
                                    11        21        31        41        51        61        71        81        91     | 100       110  
        A0N262_MOUSE      2 DIQLTQSPSSLAVSAGEKVTMSCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCHQ-YLSHTFGGGTKLEIK  112
               SCOP domains d3duuc_ C: automated matches                                                                                     SCOP domains
               CATH domains 3duuC00 C:1-106 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee.....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                3duu C    1 DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYNLRTFGGGTKLELK  106
                                    10        20       27C|||     34        44        54        64        74        84        94       104  
                                                     27A|||||                                                                               
                                                      27B||||                                                                               
                                                       27C|||                                                                               
                                                        27D||                                                                               
                                                         27E|                                                                               
                                                          27F

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with A2NU21_MOUSE | A2NU21 from UniProtKB/TrEMBL  Length:119

    Alignment length:121
                                                                                                                              119                    
                                    28        38        48        58        68        78        88        98       108       118|        -         - 
        A2NU21_MOUSE     19 EVKLVESGGGLVQPGGSLSLSCAASGFTFTDYYMSWVRQLPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCAKD--------------------    -
               SCOP domains d3duud_ D: automated matches                                                                                              SCOP domains
               CATH domains 3duuD00 D:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee......eeeeee........eee........eeeee....eeeeee...hhhhheeeeeeee.............eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3duu D    1 EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTVEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDGYYVDAMDYWGQGTSVTVSS  113
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |102       112 
                                                                              52A||                            82A||               100A|             
                                                                               52B|                             82B|                100B             
                                                                                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: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

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

1a	d3duua_	A:
1b	d3duub_	B:
1c	d3duuc_	C:
1d	d3duud_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	3duuA00	A:1-106
1b	3duuC00	C:1-106
1c	3duuB00	B:1-113
1d	3duuD00	D:1-113

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

Asymmetric Unit(hide GO term definitions)

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

Asymmetric Unit
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		Ser C:7 - Pro C:8	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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