1Q9W - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   S45-18 FAB PENTASACCHARIDE BISPHOSPHATE COMPLEX

Authors :   H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans

Date :   26 Aug 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Antigen-Binding Fragment, Fab, Anti-Cabohydrate, Anti-Lps, Antibody, Immunoglobulin, Kdo, Protein-Carbohydrate Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Germline Antibody Recognition Of Distinct Carbohydrate Epitopes.
Nat. Struct. Biol. V. 10 1019 2003
PubMed-ID: 14625588 | Reference-DOI: 10.1038/NSB1014
(for further references see the PDB file header)

Molecule 1 - S45-18 FAB (IGG1K) LIGHT CHAIN
	Chains	:	A, C
	Fragment	:	FAB1 LIGHT CHAIN KAPPA
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - S45-18 FAB (IGG1K) HEAVY CHAIN
	Chains	:	B, D
	Fragment	:	FAB1 HEAVY CHAIN G1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	GP1	1	Ligand/Ion	GLUCOSAMINE 1-PHOSPHATE
2	GP4	1	Ligand/Ion	GLUCOSAMINE 4-PHOSPHATE
3	KDO	6	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4	MG	5	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	GP1	1	Ligand/Ion	GLUCOSAMINE 1-PHOSPHATE
2	GP4	1	Ligand/Ion	GLUCOSAMINE 4-PHOSPHATE
3	KDO	3	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	GP1	-1	Ligand/Ion	GLUCOSAMINE 1-PHOSPHATE
2	GP4	-1	Ligand/Ion	GLUCOSAMINE 4-PHOSPHATE
3	KDO	3	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	GP1	1	Ligand/Ion	GLUCOSAMINE 1-PHOSPHATE
2	GP4	1	Ligand/Ion	GLUCOSAMINE 4-PHOSPHATE
3	KDO	3	Ligand/Ion	3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:30A , ARG A:30C , PRO B:14 , PHE B:97 , KDO B:302 , GP4 B:304 , GP1 B:305 , HOH B:340 , HOH B:526	BINDING SITE FOR RESIDUE KDO B 301
02	AC2	SOFTWARE	TYR B:33 , LYS B:52D , PHE B:97 , KDO B:301 , KDO B:303 , GP1 B:305 , HOH B:309A , HOH B:310A , HOH B:320 , HOH B:340 , HOH B:354 , HOH B:361 , HOH B:475	BINDING SITE FOR RESIDUE KDO B 302
03	AC3	SOFTWARE	SER A:91 , TYR A:92 , ARG A:95 , HOH A:216A , TYR B:33 , ARG B:52 , ILE B:96 , KDO B:302 , HOH B:307A , HOH B:308A , HOH B:419 , HOH B:475	BINDING SITE FOR RESIDUE KDO B 303
04	AC4	SOFTWARE	SER B:111 , KDO B:301 , GP1 B:305 , HOH B:375 , HOH B:415	BINDING SITE FOR RESIDUE GP4 B 304
05	AC5	SOFTWARE	LYS B:52D , SER B:111 , KDO B:301 , KDO B:302 , GP4 B:304 , HOH B:320 , HOH B:344 , HOH B:361 , HOH B:439	BINDING SITE FOR RESIDUE GP1 B 305
06	AC6	SOFTWARE	ASN C:30A , ARG C:30C , KDO C:312 , KDO C:313 , PHE D:97	BINDING SITE FOR RESIDUE KDO C 311
07	AC7	SOFTWARE	HOH B:423 , KDO C:311 , KDO C:313 , HOH C:379 , TYR D:33 , LYS D:52D , PHE D:97 , HOH D:214B	BINDING SITE FOR RESIDUE KDO C 312
08	AC8	SOFTWARE	SER C:91 , TYR C:92 , ARG C:95 , KDO C:311 , KDO C:312 , HOH C:316B , HOH C:317B , HOH C:318B , HOH C:378 , TYR D:33 , ARG D:52 , ILE D:96	BINDING SITE FOR RESIDUE KDO C 313
09	AC9	SOFTWARE	GLU B:56 , HOH B:376 , HOH B:377 , HOH B:378 , HOH B:379 , GLU D:56	BINDING SITE FOR RESIDUE MG B 306
10	BC1	SOFTWARE	PHE A:97 , GLU B:46 , TRP B:47 , HOH B:312	BINDING SITE FOR RESIDUE MG A 214
11	BC2	SOFTWARE	THR C:96 , PHE C:97 , HOH C:397 , GLU D:46 , TRP D:47 , HOH D:344	BINDING SITE FOR RESIDUE MG C 314
12	BC3	SOFTWARE	GLN A:6 , MET A:21 , SER A:22 , TRP A:35 , THR A:101	BINDING SITE FOR RESIDUE MG A 215
13	BC4	SOFTWARE	GLN C:6 , MET C:21 , SER C:22 , THR C:101	BINDING SITE FOR RESIDUE MG C 315

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:133	-	A:193
3	A:213	-	B:213
4	B:22	-	B:92
5	B:138	-	B:193
6	C:23	-	C:88
7	C:133	-	C:193
8	C:213	-	D:213
9	D:22	-	D:92
10	D:138	-	D:193

Asymmetric Unit

No.	Residues
1	Phe A:7	-	Pro A:8
2	Tyr A:139	-	Pro A:140
3	Phe B:144	-	Pro B:145
4	Glu B:146	-	Pro B:147
5	Trp B:186	-	Pro B:187
6	Phe C:7	-	Pro C:8
7	Tyr C:139	-	Pro C:140
8	Phe D:144	-	Pro D:145
9	Glu D:146	-	Pro D:147
10	Trp D:186	-	Pro D:187

(no "SAP(SNP)/Variant" information available for 1Q9W)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	2	A:191-197 C:191-197

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	A:191-197 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	- C:191-197

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	2	A:191-197 C:191-197

(no "Exon" information available for 1Q9W)

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:219
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:219
                                                                                                                                             1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97         
          IGKC_MOUSE      - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  106
               SCOP domains d1q9wa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1q9wa2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9wA01 A:1-107 Immunoglobulins                                                                                  1q9wA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9w A    1 DIVMSQFPSSLAVSAGEKVTMSCKSSQSLLNSRTRKSYLAWYQQKPGQFPKLLIYWAATRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                        30A|||||                                                                                                                                                                                       
                                                         30B||||                                                                                                                                                                                       
                                                          30C|||                                                                                                                                                                                       
                                                           30D||                                                                                                                                                                                       
                                                            30E|                                                                                                                                                                                       
                                                             30F

Chain A from PDB  Type:PROTEIN  Length:219
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  240
               SCOP domains d1q9wa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d1q9wa2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9wA01 A:1-107 Immunoglobulins                                                                                   1q9wA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...-..ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9w A    1 DIVMSQFPSSLAVSAGEKVTMSCKSSQSLLNSRTRKSYLAWYQQKPGQFPKLLIYWAATRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYN-LRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103       113       123       133       143       153       163       173       183       193       203       213
                                                        30A|||||                                                             93 |                                                                                                                       
                                                         30B||||                                                               94                                                                                                                       
                                                          30C|||                                                                                                                                                                                        
                                                           30D||                                                                                                                                                                                        
                                                            30E|                                                                                                                                                                                        
                                                             30F

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with I6L985_MOUSE | I6L985 from UniProtKB/TrEMBL  Length:469

    Alignment length:228
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
        I6L985_MOUSE     20 EVNLVESGGGLVQPGGSLRLSCAASGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCARDRRSSYYYSGTSFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDC  247
               SCOP domains d1q9wb1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                                d1q9wb2 B:112-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1q9wB01 B:1-111 Immunoglobulins                                                                                               1q9wB02 B:112-210 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee....--........ee...eeeee........eeeee..........eeeeeeeeeee.....eee.........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q9w B    1 EVILVESGGGLVQPGGSLRLSCSTSGFTFTDYYMSWVRQPPGKALEWLGFIRNKPKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCVRDIYS--FGSRDGMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  213
                                    10        20        30        40        50  ||||| 55        65        75       |84        94  ||  |100|||||  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A||||                            82A            96A| 97   |||||                                                                                                                 
                                                                               52B|||                                            96B   100A||||                                                                                                                 
                                                                                52C||                                                   100B|||                                                                                                                 
                                                                                 52D|                                                    100C||                                                                                                                 
                                                                                  52E                                                     100D|                                                                                                                 
                                                                                                                                           100E

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:219
                                                                                                                                             1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97         
          IGKC_MOUSE      - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  106
               SCOP domains d1q9wc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1q9wc2 C:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9wC01 C:1-107 Immunoglobulins                                                                                  1q9wC02 C:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh....eeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9w C    1 DIVMSQFPSSLAVSAGEKVTMSCKSSQSLLNSRTRKSYLAWYQQKPGQFPKLLIYWAATRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                        30A|||||                                                                                                                                                                                       
                                                         30B||||                                                                                                                                                                                       
                                                          30C|||                                                                                                                                                                                       
                                                           30D||                                                                                                                                                                                       
                                                            30E|                                                                                                                                                                                       
                                                             30F

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  240
               SCOP domains d1q9wc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d1q9wc2 C:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1q9wC01 C:1-107 Immunoglobulins                                                                                   1q9wC02 C:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...-..ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh....eeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1q9w C    1 DIVMSQFPSSLAVSAGEKVTMSCKSSQSLLNSRTRKSYLAWYQQKPGQFPKLLIYWAATRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYN-LRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103       113       123       133       143       153       163       173       183       193       203       213
                                                        30A|||||                                                             93 |                                                                                                                       
                                                         30B||||                                                               94                                                                                                                       
                                                          30C|||                                                                                                                                                                                        
                                                           30D||                                                                                                                                                                                        
                                                            30E|                                                                                                                                                                                        
                                                             30F

Chain D from PDB  Type:PROTEIN  Length:226
 aligned with I6L985_MOUSE | I6L985 from UniProtKB/TrEMBL  Length:469

    Alignment length:228
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
        I6L985_MOUSE     20 EVNLVESGGGLVQPGGSLRLSCAASGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCARDRRSSYYYSGTSFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDC  247
               SCOP domains d1q9wd1 D:1-111 Immunoglobulin heavy chain variable domain, VH                                                                d1q9wd2 D:112-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1q9wD01 D:1-111 Immunoglobulins                                                                                               1q9wD02 D:112-209 Immunoglobulins                                                                 ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee....--........ee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeee..........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1q9w D    1 EVILVESGGGLVQPGGSLRLSCSTSGFTFTDYYMSWVRQPPGKALEWLGFIRNKPKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCVRDIYS--FGSRDGMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  213
                                    10        20        30        40        50  ||||| 55        65        75       |84        94  ||  |100|||||  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A||||                            82A            96A| 97   |||||                                                                                                                 
                                                                               52B|||                                            96B   100A||||                                                                                                                 
                                                                                52C||                                                   100B|||                                                                                                                 
                                                                                 52D|                                                    100C||                                                                                                                 
                                                                                  52E                                                     100D|                                                                                                                 
                                                                                                                                           100E

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(

)

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	1q9wA02	A:108-210
1b	1q9wB02	B:112-210
1c	1q9wD02	D:112-209
1d	1q9wC02	C:108-210
1e	1q9wA01	A:1-107
1f	1q9wC01	C:1-107
1g	1q9wB01	B:1-111
1h	1q9wD01	D:1-111

(no "Pfam Domain" information available for 1Q9W)

Asymmetric Unit(hide GO term definitions)

Chain A,C (IGKC_MOUSE | P01837)

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.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,C (Q52L64_MOUSE | Q52L64)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Chain B,D (I6L985_MOUSE | I6L985)

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	Cis Peptide Bonds
		Glu B:146 - Pro B:147	[ RasMol ]
		Glu D:146 - Pro D:147	[ RasMol ]
		Phe A:7 - Pro A:8	[ RasMol ]
		Phe B:144 - Pro B:145	[ RasMol ]
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		Phe D:144 - Pro D:145	[ RasMol ]
		Trp B:186 - Pro B:187	[ RasMol ]
		Trp D:186 - Pro D:187	[ RasMol ]
		Tyr A:139 - Pro A:140	[ RasMol ]
		Tyr C:139 - Pro C:140	[ RasMol ]

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		Biological Unit 3	[ Jena3D ]

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	1q9w
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	I6L985_MOUSE \| I6L985
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	IGKC_MOUSE \| P01837
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	Q52L64_MOUSE \| Q52L64
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	I6L985_MOUSE \| I6L985
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	IGKC_MOUSE \| P01837
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	Q52L64_MOUSE \| Q52L64
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1q9k	RELATED AB S25-2 UNLIGANDED
1q9l	S25-2 FAB UNLIGANDED DIFFERENT CRYSTAL FORM
1q9o	THE SAME ANTIBODY S45-18, BUT UNLIGANDED
1q9q	RELATED AB S25-2 LIGANDED WITH A(2-8)-A(2-4) KDO TRISACCHARIDE
1q9r	RELATED AB S25-2 LIGANDED WITH A(2-8) KDO DISACCHARIDE
1q9t	RELATED AB S25-2 LIGANDED WITH A(2-4) KDO DISACCHARIDE
1q9v	RELATED AB S25-2 LIGANDED WITH KDO MONOSACCHARIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (10, 10)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File