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Title :   CRYSTAL STRUCTURE OF SAG173-04

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 :   1.86

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 SAG173-04
	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, 6)

No.	Name	Count	Type	Full Name
1	KDO	2	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2	MG	2	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 (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:30A , SER A:91 , TYR A:92 , ARG A:95 , HOH A:315 , HOH A:348 , HOH A:407 , TYR B:33 , PHE B:50 , ARG B:52 , ASP B:99	BINDING SITE FOR RESIDUE KDO A 303
2	AC2	SOFTWARE	LYS C:30A , SER C:91 , TYR C:92 , ARG C:95 , HOH C:124 , TYR D:33 , PHE D:50 , ARG D:52 , ASP D:99 , HOH D:371 , HOH D:383	BINDING SITE FOR RESIDUE KDO D 303
3	AC3	SOFTWARE	GLN A:79 , HOH A:313 , HOH A:332 , HOH A:335 , HOH A:357 , HOH A:388	BINDING SITE FOR RESIDUE MG A 107
4	AC4	SOFTWARE	HOH A:321 , HOH A:331 , GLN C:79 , HOH C:153 , HOH C:217	BINDING SITE FOR RESIDUE MG C 108
5	AC5	SOFTWARE	LYS D:52D , TYR D:97	BINDING SITE FOR RESIDUE PG4 D 304
6	AC6	SOFTWARE	LYS B:52D , PRO C:40	BINDING SITE FOR RESIDUE PG4 B 112

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 3DUR)

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

(no "Exon" information available for 3DUR)

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 A2N494_MOUSE | A2N494 from UniProtKB/TrEMBL  Length:114

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
        A2N494_MOUSE      1 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSYPRTFGGGTKLEIK  113
               SCOP domains d3dura_ A: automated matches                                                                                      SCOP domains
               CATH domains 3durA00 A:1-106 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee...-..ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                3dur A    1 DIVMTQSPSSLAVSAGEKVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYN-LRTFGGGTKLELK  106
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103   
                                                        30A|||||                                                             93 |            
                                                         30B||||                                                               94            
                                                          30C|||                                                                             
                                                           30D||                                                                             
                                                            30E|                                                                             
                                                             30F

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 d3durb_ B: automated matches                                                                                              SCOP domains
               CATH domains 3durB00 B:1-111 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3dur B    1 EVQLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFSISRDNSQSILYLQMNTLRAEDSATYYCARDGYYADAMDYWGQGTSVTVSS  111
                                    10        20        30        40        50  ||||| 55        65        75      ||84        94   |  100E       110 
                                                                              52A||||                           81A|             97A   |||           
                                                                               52B|||                            82A                100C||           
                                                                                52C||                                                100D|           
                                                                                 52D|                                                 100E           
                                                                                  52E

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with A2N494_MOUSE | A2N494 from UniProtKB/TrEMBL  Length:114

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
        A2N494_MOUSE      1 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSYPRTFGGGTKLEIK  113
               SCOP domains d3durc_ C: automated matches                                                                                      SCOP domains
               CATH domains 3durC00 C:1-106 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee...-..ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                3dur C    1 DIVMTQSPSSLAVSAGEKVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYN-LRTFGGGTKLELK  106
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103   
                                                        30A|||||                                                             93 |            
                                                         30B||||                                                               94            
                                                          30C|||                                                                             
                                                           30D||                                                                             
                                                            30E|                                                                             
                                                             30F

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 d3durd_ D: automated matches                                                                                              SCOP domains
               CATH domains 3durD00 D:1-111 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                3dur D    1 EVQLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFSISRDNSQSILYLQMNTLRAEDSATYYCARDGYYADAMDYWGQGTSVTVSS  111
                                    10        20        30        40        50  ||||| 55        65        75    |   84        94   |  100E       110 
                                                                              52A||||                         80A                97A   |||           
                                                                               52B|||                                               100C||           
                                                                                52C||                                                100D|           
                                                                                 52D|                                                 100E           
                                                                                  52E

Legend:		→ Mismatch	(orange background)
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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 '\|'

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	d3dura_	A:
1b	d3durb_	B:
1c	d3durc_	C:
1d	d3durd_	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	3durA00	A:1-106
1b	3durC00	C:1-106
1c	3durB00	B:1-111
1d	3durD00	D:1-111

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

Asymmetric Unit(hide GO term definitions)

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

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (3, 6)

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