4D9R - JenaLib

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)

Title :   INHIBITING ALTERNATIVE PATHWAY COMPLEMENT ACTIVATION BY TARGETING THE EXOSITE ON FACTOR D

Authors :   J. M. Murray, C. Wiesmann

Date :   11 Jan 12 (Deposition) - 22 Feb 12 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

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

Keywords :   Factor D, Complement, Antibody, Exosite, Fab, Chymotrypsin, Protease, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. J. Katschke, P. Wu, R. Ganesan, R. F. Kelley, M. A. Mathieu, P. E. Hass J. Murray, D. Kirchhofer, C. Wiesmann, M. Van Lookeren Campagne
Inhibiting Alternative Pathway Complement Activation By Targeting The Factor D Exosite.
J. Biol. Chem. V. 287 12886 2012
PubMed-ID: 22362762 | Reference-DOI: 10.1074/JBC.M112.345082

Molecule 1 - COMPLEMENT FACTOR D
	Chains	:	A, B
	EC Number	:	3.4.21.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CFD, DF, FACTOR D, PFD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ADIPSIN, C3 CONVERTASE ACTIVATOR, PROPERDIN FACTOR D

Molecule 2 - FAB LIGHT CHAIN
	Chains	:	L, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	IGKC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FAB HEAVY CHAIN
	Chains	:	H, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	IGHG1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	D	E	H	L
Biological Unit 1 (1x)	:	A				H	L
Biological Unit 2 (1x)	:		B	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG D:55 , HOH D:408 , ASN E:109	BINDING SITE FOR RESIDUE CL D 301
2	AC2	SOFTWARE	ASP D:92	BINDING SITE FOR RESIDUE CL D 302

Asymmetric Unit

No.	Residues
1	A:42	-	A:58
2	A:136	-	A:201
3	A:168	-	A:182
4	A:191	-	A:220
5	B:42	-	B:58
6	B:136	-	B:201
7	B:168	-	B:182
8	B:191	-	B:220
9	D:23	-	D:88
10	D:134	-	D:194
11	E:22	-	E:96
12	E:148	-	E:204
13	H:22	-	H:96
14	H:148	-	H:204
15	L:23	-	L:88
16	L:134	-	L:194
17	L:214	-	H:224

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Leu L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:154	-	Pro H:155
5	Glu H:156	-	Pro H:157
6	Phe E:154	-	Pro E:155
7	Glu E:156	-	Pro E:157
8	Ser D:7	-	Pro D:8
9	Leu D:94	-	Pro D:95
10	Tyr D:140	-	Pro D:141

Asymmetric Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	D/L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	D/L	V	191	L
3	UniProt	VAR_034866	V	213	G	CFAD_HUMAN	Disease (CFDD)	267606720	A/B	V	200	G
4	UniProt	VAR_034867	C	214	R	CFAD_HUMAN	Disease (CFDD)	267606721	A/B	C	201	R
5	UniProt	VAR_034868	I	248	M	CFAD_HUMAN	Polymorphism	2230216	A/B	I	238	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	L	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	L	V	191	L
3	UniProt	VAR_034866	V	213	G	CFAD_HUMAN	Disease (CFDD)	267606720	A	V	200	G
4	UniProt	VAR_034867	C	214	R	CFAD_HUMAN	Disease (CFDD)	267606721	A	C	201	R
5	UniProt	VAR_034868	I	248	M	CFAD_HUMAN	Polymorphism	2230216	A	I	238	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066403	W	41	R	IGKC_HUMAN	Disease (IGKCD)	---	D	W	148	R
2	UniProt	VAR_003897	V	84	L	IGKC_HUMAN	Polymorphism	---	D	V	191	L
3	UniProt	VAR_034866	V	213	G	CFAD_HUMAN	Disease (CFDD)	267606720	B	V	200	G
4	UniProt	VAR_034867	C	214	R	CFAD_HUMAN	Disease (CFDD)	267606721	B	C	201	R
5	UniProt	VAR_034868	I	248	M	CFAD_HUMAN	Polymorphism	2230216	B	I	238	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CFAD_HUMAN	26-253	2	A:16-243 B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CFAD_HUMAN	62-67	2	A:53-58 B:53-58
3	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	2	D:192-198 L:192-198
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CFAD_HUMAN	202-213	2	A:189-200 B:189-200

Biological Unit 1 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CFAD_HUMAN	26-253	1	A:16-243 -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CFAD_HUMAN	62-67	1	A:53-58 -
3	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	1	- L:192-198
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CFAD_HUMAN	202-213	1	A:189-200 -

Biological Unit 2 (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CFAD_HUMAN	26-253	1	- B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CFAD_HUMAN	62-67	1	- B:53-58
3	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_HUMAN	85-91	1	D:192-198 -
4	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CFAD_HUMAN	202-213	1	- B:189-200

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000327726	1	ENSE00001231576	chr19:859665-859744	80	CFAD_HUMAN	1-19	19	0	-	-
1.2	ENST00000327726	2	ENSE00001231561	chr19:860617-860773	157	CFAD_HUMAN	19-71	53	2	A:16-61A (gaps) B:16-61A (gaps)	47 47
1.3	ENST00000327726	3	ENSE00001231555	chr19:860861-861005	145	CFAD_HUMAN	71-119	49	2	A:61A-107 B:61A-107	49 49
1.4	ENST00000327726	4	ENSE00001374327	chr19:861699-861956	258	CFAD_HUMAN	120-205	86	2	A:108-192 (gaps) B:108-192 (gaps)	89 89
1.5	ENST00000327726	5	ENSE00001354943	chr19:863092-863606	515	CFAD_HUMAN	206-253	48	2	A:193-243 (gaps) B:193-243 (gaps)	52 52

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:228
 aligned with CFAD_HUMAN | P00746 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
          CFAD_HUMAN     26 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA  253
               SCOP domains d4d9ra_ A: Factor D                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhhh......eeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeee..............eeee..eeeeee.............eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GR---------------------------------M----- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 26-253                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61A (gaps) UniProt: 19-71 ------------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 120-205                                      Exon 1.5  PDB: A:193-243 (gaps) UniProt: 206-253 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:61A-107 UniProt: 71-119         -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                4d9r A   16 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA  243
                                    25        35|       46        56     |||63        73        83        93       103       113 ||   124A     | 133       143   ||  154       164      |172       182       192       202|      216       225       235        
                                              35|                      61A||                                                   115|   124A  129A               147|                  170A|                             202|             223A                    
                                               37                       61B|                                                    118                             149                   170B                              207                                     
                                                                         61C

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with CFAD_HUMAN | P00746 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
          CFAD_HUMAN     26 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA  253
               SCOP domains d4d9rb_ B: Factor D                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhh.......eeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhhh...........eeee..............eee....eeeee.............eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GR---------------------------------M----- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 26-253                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:16-61A (gaps) UniProt: 19-71 ------------------------------------------------Exon 1.4  PDB: B:108-192 (gaps) UniProt: 120-205                                      Exon 1.5  PDB: B:193-243 (gaps) UniProt: 206-253 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: B:61A-107 UniProt: 71-119         -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                4d9r B   16 ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA  243
                                    25        35|       46        56     |||63        73        83        93       103       113 ||   124A     | 133       143   ||  154       164      |172       182       192       202|      216       225       235        
                                              35|                      61A||                                                   115|   124A  129A               147|                  170A|                             202|             223A                    
                                               37                       61B|                                                    118                             149                   170B                              207                                     
                                                                         61C

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with IGKC_HUMAN | P01834 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:213
                                                                                                                                       1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103   
          IGKC_HUMAN      - -----------------------------------------------------------------------------------------------------------RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  106
               SCOP domains d4d9rd1 D:1-107 automated matches                                                                          d4d9rd2 D:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------L---------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d9r D    1 DIQVTQSPSSLSASVGDRVTITCITSTDIDDDMNWYQQKPGKVPKLLISGGNTLRPGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain E from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.....ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4d9r E    1 EVQLVQSGPELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGETTYADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCEREGGVNNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  222
                                    10        20        30        40        50        60        70        80        90       100||     116       126       136       146       156       166       176       186       196       206       216      
                                                                                                                              101|                                                                                                                  
                                                                                                                               108

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.....ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d9r H    1 EVQLVQSGPELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGETTYADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCEREGGVNNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  224
                                    10        20        30        40        50        60        70        80        90       100||     116       126       136       146       156       166       176       186       196       206       216        
                                                                                                                              101|                                                                                                                    
                                                                                                                               108

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_HUMAN | P01834 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:214
                                                                                                                                       1                                                                                                          
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103    
          IGKC_HUMAN      - -----------------------------------------------------------------------------------------------------------RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  107
               SCOP domains d4d9rl1 L:1-107 automated matches                                                                          d4d9rl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------L----------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d9r L    1 DIQVTQSPSSLSASVGDRVTITCITSTDIDDDMNWYQQKPGKVPKLLISGGNTLRPGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    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: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d4d9rd1	D:1-107
1b	d4d9rl1	L:1-107

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

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

2a	d4d9rd2	D:108-213
2b	d4d9rl2	L:108-214

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Factor D (12)

Human (Homo sapiens) [TaxId: 9606] (12)

3a	d4d9ra_	A:
3b	d4d9rb_	B:

(no "CATH Domain" information available for 4D9R)

(no "Pfam Domain" information available for 4D9R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CFAD_HUMAN | P00746)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	GO:0006957	complement activation, alternative pathway	Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.

Chain D,L (IGKC_HUMAN | P01834)

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.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	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:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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.

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	4d9r
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	IGKC_HUMAN \| P01834
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	IGKC_HUMAN \| P01834
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4d9q	CYNO FACTOR D IN COMPLEX WITH ANTI-FACTOR D

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (17, 17)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 10)

PROSITE Motifs (4, 8)

Exons (4, 8)

Sequences/Alignments

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SCOP Domains (3, 6)

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Gene Ontology (33, 59)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File