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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED 5C8 ANTIBODY

Authors :   M. Karpusas, J. Lucci, J. Ferrant, C. Benjamin, Y. -M. Hsu

Date :   20 Mar 01 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,C,H,K,L,M,X,Y

Keywords :   Beta-Sheet Sandwich, Immunoglobulin, Cytokine/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Karpusas, J. Lucci, J. Ferrant, C. Benjamin, F. R. Taylor, K. Strauch, E. Garber, Y. M. Hsu
Structure Of Cd40 Ligand In Complex With The Fab Fragment Of A Neutralizing Humanized Antibody.
Structure V. 9 321 2001
PubMed-ID: 11525169 | Reference-DOI: 10.1016/S0969-2126(01)00590-1
(for further references see the PDB file header)

Molecule 1 - CD40 LIGAND
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Fragment	:	RESIDUES 116-261
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CD40-L

Molecule 2 - IMMUNOGLOBULIN H
	Cell Line	:	NSO MYELOMA
	Chains	:	H, K, X
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - IMMUNOGLOBULIN L
	Cell Line	:	NSO MYELOMA
	Chains	:	L, M, Y
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6	7	8	9
Asymmetric/Biological Unit	:	A	B	C	H	K	L	M	X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP H:100 , ASP H:104 , ASP H:106 , LYS L:53 , GLU L:59	BINDING SITE FOR RESIDUE ZN H 498
2	AC2	SOFTWARE	ASP K:100 , ASP K:104 , ASP K:106 , LYS M:53 , GLU M:59	BINDING SITE FOR RESIDUE ZN K 499
3	AC3	SOFTWARE	ASP X:100 , ASP X:104 , ASP X:106 , LYS Y:53 , GLU Y:59	BINDING SITE FOR RESIDUE ZN X 500

Asymmetric/Biological Unit

No.	Residues
1	A:178	-	A:218
2	B:178	-	B:218
3	C:178	-	C:218
4	H:22	-	H:96
5	H:145	-	H:201
6	K:22	-	K:96
7	K:145	-	K:201
8	L:23	-	L:92
9	L:138	-	L:198
10	M:23	-	M:92
11	M:138	-	M:198
12	X:22	-	X:96
13	X:145	-	X:201
14	Y:23	-	Y:92
15	Y:138	-	Y:198

Asymmetric/Biological Unit

No.	Residues
1	Lys A:216	-	Pro A:217
2	Lys B:216	-	Pro B:217
3	Lys C:216	-	Pro C:217
4	Phe H:151	-	Pro H:152
5	Glu H:153	-	Pro H:154
6	Ser L:7	-	Pro L:8
7	Ile L:98	-	Pro L:99
8	Tyr L:144	-	Pro L:145
9	Phe K:151	-	Pro K:152
10	Glu K:153	-	Pro K:154
11	Ser M:7	-	Pro M:8
12	Ile M:98	-	Pro M:99
13	Tyr M:144	-	Pro M:145
14	Phe X:151	-	Pro X:152
15	Glu X:153	-	Pro X:154
16	Ser Y:7	-	Pro Y:8
17	Ile Y:98	-	Pro Y:99
18	Tyr Y:144	-	Pro Y:145

Asymmetric/Biological Unit (29, 87)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_007514	A	123	E	CD40L_HUMAN	Disease (HIGM1)	104894778	A/B/C	A	123	E
02	UniProt	VAR_017926	H	125	R	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	H	125	R
03	UniProt	VAR_007515	V	126	A	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	V	126	A
04	UniProt	VAR_017931	V	126	D	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	V	126	D
05	UniProt	VAR_007517	W	140	C	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	W	140	C
06	UniProt	VAR_007518	W	140	G	CD40L_HUMAN	Disease (HIGM1)	104894777	A/B/C	W	140	G
07	UniProt	VAR_007519	W	140	R	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	W	140	R
08	UniProt	VAR_017932	K	143	T	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	K	143	T
09	UniProt	VAR_007520	G	144	E	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	G	144	E
10	UniProt	VAR_017922	T	147	N	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	T	147	N
11	UniProt	VAR_007521	L	155	P	CD40L_HUMAN	Disease (HIGM1)	104894769	A/B/C	L	155	P
12	UniProt	VAR_017923	Y	170	C	CD40L_HUMAN	Disease (HIGM1)	756468554	A/B/C	Y	170	C
13	UniProt	VAR_017933	A	173	D	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	A	173	D
14	UniProt	VAR_017927	Q	174	R	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	Q	174	R
15	UniProt	VAR_017934	T	176	I	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	T	176	I
16	UniProt	VAR_017935	L	195	P	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	L	195	P
17	UniProt	VAR_017936	A	208	D	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	A	208	D
18	UniProt	VAR_007522	T	211	N	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	T	211	N
19	UniProt	VAR_007523	G	219	R	CD40L_HUMAN	Polymorphism	148594123	A/B/C	G	219	R
20	UniProt	VAR_017937	H	224	Y	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	H	224	Y
21	UniProt	VAR_017938	G	226	A	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	G	226	A
22	UniProt	VAR_007524	G	227	V	CD40L_HUMAN	Disease (HIGM1)	104894768	A/B/C	G	227	V
23	UniProt	VAR_007526	L	231	S	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	L	231	S
24	UniProt	VAR_007527	A	235	P	CD40L_HUMAN	Disease (HIGM1)	104894771	A/B/C	A	235	P
25	UniProt	VAR_017939	V	237	E	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	V	237	E
26	UniProt	VAR_007528	T	254	M	CD40L_HUMAN	Disease (HIGM1)	193922136	A/B/C	T	254	M
27	UniProt	VAR_017940	G	257	D	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	G	257	D
28	UniProt	VAR_017928	G	257	S	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	G	257	S
29	UniProt	VAR_017924	L	258	S	CD40L_HUMAN	Disease (HIGM1)	---	A/B/C	L	258	S

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

Asymmetric/Biological Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	CD40L_HUMAN	123-261	3	A:123-261 B:123-261 C:123-261
2	TNF_1	PS00251	TNF family signature.	CD40L_HUMAN	161-177	3	A:161-177 B:161-177 C:161-177

Asymmetric/Biological Unit (2, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000370629	1a	ENSE00001453187	X:135730352-135730563	212	CD40L_HUMAN	1-52	52	0	-	-
1.2	ENST00000370629	2	ENSE00000677016	X:135732425-135732556	132	CD40L_HUMAN	53-96	44	0	-	-
1.3	ENST00000370629	3	ENSE00000677017	X:135736532-135736589	58	CD40L_HUMAN	97-116	20	0	-	-
1.4	ENST00000370629	4	ENSE00000677018	X:135738515-135738577	63	CD40L_HUMAN	116-137	22	3	A:119-137 B:119-137 C:119-137	19 19 19
1.5	ENST00000370629	5	ENSE00001125156	X:135741198-135742549	1352	CD40L_HUMAN	137-261	125	3	A:137-261 B:137-261 C:137-261	125 125 125

Asymmetric/Biological 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:143
 aligned with CD40L_HUMAN | P29965 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:143
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258   
          CD40L_HUMAN   119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
               SCOP domains d1i9ra_ A: Extracellular domain of CD40 ligand                                                                                                  SCOP domains
               CATH domains 1i9rA00 A:119-261  [code=2.60.120.40, no name defined]                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........eee.....ee....eeee...eeee...eeeeeeeeeeeee.........eeeeeeee......eeeeeeee........eeeeeee..eeee....eeeeee.hhhh........eeeeee. Sec.struct. author
             SAPs(SNPs) (1) ----E-RA-------------C--TE--N-------P--------------C--DR-I------------------P------------D--N-------R----Y-AV---S---P-E----------------M--DS--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------D-------------G--------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------R------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ----TNF_2  PDB: A:123-261 UniProt: 123-261                                                                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4           ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.5  PDB: A:137-261 UniProt: 137-261                                                                                     Transcript 1 (2)
                 1i9r A 119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with CD40L_HUMAN | P29965 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:143
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258   
          CD40L_HUMAN   119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
               SCOP domains d1i9rb_ B: Extracellular domain of CD40 ligand                                                                                                  SCOP domains
               CATH domains 1i9rB00 B:119-261  [code=2.60.120.40, no name defined]                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........eee.....ee....eeee...eeee...eeeeeeeeeeeee.........eeeeeeee.......eeeeeee........eeeeeee..eeee....eeeeee.hhhh........eeeeee. Sec.struct. author
             SAPs(SNPs) (1) ----E-RA-------------C--TE--N-------P--------------C--DR-I------------------P------------D--N-------R----Y-AV---S---P-E----------------M--DS--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------D-------------G--------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------R------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ----TNF_2  PDB: B:123-261 UniProt: 123-261                                                                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4           ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.5  PDB: B:137-261 UniProt: 137-261                                                                                     Transcript 1 (2)
                 1i9r B 119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with CD40L_HUMAN | P29965 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:143
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258   
          CD40L_HUMAN   119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
               SCOP domains d1i9rc_ C: Extracellular domain of CD40 ligand                                                                                                  SCOP domains
               CATH domains 1i9rC00 C:119-261  [code=2.60.120.40, no name defined]                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........eee.....ee....eeee...eeee...eeeeeeeeeeeee.........eeeeeee.......eeeeeeee........eeeeeee..eeee....eeeeee.hhhh........eeeeee. Sec.struct. author
             SAPs(SNPs) (1) ----E-RA-------------C--TE--N-------P--------------C--DR-I------------------P------------D--N-------R----Y-AV---S---P-E----------------M--DS--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------D-------------G--------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------R------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) ----TNF_2  PDB: C:123-261 UniProt: 123-261                                                                                                      PROSITE (1)
                PROSITE (2) ------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4           ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.5  PDB: C:137-261 UniProt: 137-261                                                                                     Transcript 1 (2)
                 1i9r C 119 NPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1i9rh1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1i9rh2 H:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1i9rH01 H:1-112 Immunoglobulins                                                                                 1i9rH02 H:113-219 Immunoglobulins                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh....eeee....eeeeee...hhhhheeeeeeeee...eeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r H   1 QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNFNEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain K from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1i9rk1 K:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1i9rk2 K:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1i9rK01 K:1-112 Immunoglobulins                                                                                 1i9rK02 K:113-219 Immunoglobulins                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh.....ee.hhh.eeeeeee..hhhhheeeeeeeee...eeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r K   1 QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNFNEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1i9rl1 L:1-111 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1i9rl2 L:112-215 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1i9rL01 L:1-112 Immunoglobulins                                                                                 1i9rL02 L:113-215 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....ee............eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r L   1 DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLESGVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEIPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1i9rm1 M:1-111 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1i9rm2 M:112-215 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1i9rM01 M:1-112 Immunoglobulins                                                                                 1i9rM02 M:113-215 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee............eeeeee......eeeee...ee.........eeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....ee............eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r M   1 DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLESGVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEIPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain X from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1i9rx1 X:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1i9rx2 X:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1i9rX01 X:1-112 Immunoglobulins                                                                                 1i9rX02 X:113-219 Immunoglobulins                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh.....eee....eeeeee...hhhhheeeeeeeee...eeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r X   1 QVQLVQSGAEVVKPGASVKLSCKASGYIFTSYYMYWVKQAPGQGLEWIGEINPSNGDTNFNEKFKSKATLTVDKSASTAYMELSSLRSEDTAVYYCTRSDGRNDMDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain Y from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1i9ry1 Y:1-111 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1i9ry2 Y:112-215 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1i9rY01 Y:1-112 Immunoglobulins                                                                                 1i9rY02 Y:113-215 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee............eeeeee......eeeee...ee.........eeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee...................ee............eeeeeeeeeehhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9r Y   1 DIVLTQSPATLSVSPGERATISCRASQRVSSSTYSYMHWYQQKPGQPPKLLIKYASNLESGVPARFSGSGSGTDFTLTISSVEPEDFATYYCQHSWEIPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 215
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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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	1i9rL02	L:113-215
1b	1i9rL01	L:1-112
1c	1i9rM01	M:1-112
1d	1i9rY01	Y:1-112
1e	1i9rH02	H:113-219
1f	1i9rK02	K:113-219
1g	1i9rX02	X:113-219
1h	1i9rH01	H:1-112
1i	1i9rK01	K:1-112
1j	1i9rX01	X:1-112
1k	1i9rM02	M:113-215
1l	1i9rY02	Y:113-215

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.40, no name defined] (56)

Human (Homo sapiens) (38)

2a	1i9rA00	A:119-261
2b	1i9rB00	B:119-261
2c	1i9rC00	C:119-261

(no "Pfam Domain" information available for 1I9R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (CD40L_HUMAN | P29965)

molecular function
	GO:0005174	CD40 receptor binding	Interacting selectively and non-covalently with CD40, a receptor found on the surface of all B-lymphocytes.
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005164	tumor necrosis factor receptor binding	Interacting selectively and non-covalently with the tumor necrosis factor receptor.
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:0042100	B cell proliferation	The expansion of a B cell population by cell division. Follows B cell activation.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0007257	activation of JUN kinase activity	The initiation of the activity of the inactive enzyme JUN kinase (JNK).
	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:0048305	immunoglobulin secretion	The regulated release of immunoglobulins from a B cell or plasma cell, whose mechanism includes the use of alternate polyadenylylation signals to favor the biosynthesis of secreted forms of immunoglobulin over membrane-bound immunoglobulin.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0045190	isotype switching	The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
	GO:0007159	leukocyte cell-cell adhesion	The attachment of a leukocyte to another cell via adhesion molecules.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:2000353	positive regulation of endothelial cell apoptotic process	Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
	GO:0032733	positive regulation of interleukin-10 production	Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
	GO:0032735	positive regulation of interleukin-12 production	Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
	GO:0032753	positive regulation of interleukin-4 production	Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
	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:0051023	regulation of immunoglobulin secretion	Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
	GO:0033209	tumor necrosis factor-mediated signaling pathway	A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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: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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric/Biological Unit
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		Tyr Y:144 - Pro Y:145	[ RasMol ]

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	1i9r
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	CD40L_HUMAN \| P29965	:	1aly 3lkj 3qd6

(no "Related Entries Specified in the PDB File" available for 1I9R)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (15, 15)

Cis Peptide Bonds (18, 18)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (29, 87)

PROSITE Motifs (2, 6)

Exons (2, 6)

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SCOP Domains (5, 15)

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