3V56 - 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)

Biological Unit 3 (Jmol Viewer)

Title :   RE-REFINEMENT OF PDB ENTRY 1OSG - COMPLEX BETWEEN BAFF AND A BR3 DERIVED PEPTIDE PRESENTED IN A BETA-HAIRPIN SCAFFOLD - REVEALS AN ADDITONAL COPY OF THE PEPTIDE.

Authors :   O. S. Smart, T. O. Womack, C. Flensburg, P. Keller, A. Sharff, W. Paciore C. Vonrhein, G. Bricogne

Date :   16 Dec 11 (Deposition) - 28 Mar 12 (Release) - 20 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,Z
Biol. Unit 1: A,B,C,G,H,I  (1x)
Biol. Unit 2: D,E,F,J,K,L  (1x)
Biol. Unit 3: Z  (1x)

Keywords :   Jelly-Roll, Beta Hairpin, Protein-Peptide Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. S. Smart, T. O. Womack, C. Flensburg, P. Keller, W. Paciorek, A. Sharff, C. Vonrhein, G. Bricogne
Exploiting Structure Similarity In Refinement: Automated Nc And Target-Structure Restraints In Buster.
Acta Crystallogr. , Sect. D V. 68 368 2012
PubMed-ID: 22505257 | Reference-DOI: 10.1107/S0907444911056058

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	B LYMPHOCYTE STIMULATOR, BLYS, B-CELL-ACTIVATING FACTOR, BAFF, DENDRITIC CELL-DERIVED TNF-LIKE MOLECULE, TNF- AND APOL-RELATED LEUKOCYTE EXPRESSED LIGAND 1, TALL-1, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B, SOLUBLE FORM

Molecule 2 - BR3 DERIVED PEPTIVE
	Chains	:	G, H, I, J, K, L, Z
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10	11	12	13
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L	Z
Biological Unit 1 (1x)	:	A	B	C				G	H	I
Biological Unit 2 (1x)	:				D	E	F				J	K	L
Biological Unit 3 (1x)	:													Z

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	7	Mod. Amino Acid	AMINO GROUP
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	3	Mod. Amino Acid	AMINO GROUP
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ACE	-1	Mod. Amino Acid	ACETYL GROUP
2	NH2	3	Mod. Amino Acid	AMINO GROUP
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ACE	-1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:234 , ASN A:235 , ASN A:243 , GLN B:234 , ASN B:235 , ASN B:243 , GLN C:234 , ASN C:235 , ASN C:243	BINDING SITE FOR RESIDUE SO4 A 499
2	AC2	SOFTWARE	GLN D:234 , ASN D:235 , ASN D:243 , GLN E:234 , ASN E:235 , ASN E:243 , GLN F:234 , ASN F:235 , ASN F:243	BINDING SITE FOR RESIDUE SO4 D 499

Asymmetric Unit

No.	Residues
1	A:232	-	A:245
2	B:232	-	B:245
3	C:232	-	C:245
4	D:232	-	D:245
5	E:232	-	E:245
6	F:232	-	F:245
7	G:23	-	G:34
8	H:23	-	H:34
9	I:23	-	I:34
10	J:23	-	J:34
11	K:23	-	K:34
12	L:23	-	L:34
13	Z:23	-	Z:34

(no "Cis Peptide Bond" information available for 3V56)

(no "SAP(SNP)/Variant" information available for 3V56)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TN13B_HUMAN	148-284	6	A:148-284 B:148-284 C:148-284 D:148-284 E:148-284 F:148-284

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TN13B_HUMAN	148-284	3	A:148-284 B:148-284 C:148-284 - - -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TN13B_HUMAN	148-284	3	- - - D:148-284 E:148-284 F:148-284

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TNF_2	PS50049	TNF family profile.	TN13B_HUMAN	148-284	0	- - - - - -

Asymmetric Unit (6, 37)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000291232	1	ENSE00001175504	chr22:42322822-42322642	181	TR13C_HUMAN	1-46	46	7	G:22-35 (gaps) H:23-35 (gaps) I:23-35 (gaps) J:23-35 (gaps) K:23-35 (gaps) L:23-35 (gaps) Z:23-35 (gaps)	19 18 18 18 18 18 18
1.2	ENST00000291232	2	ENSE00001048605	chr22:42322335-42322105	231	TR13C_HUMAN	46-123	78	0	-	-
1.3	ENST00000291232	3	ENSE00001201908	chr22:42321558-42321045	514	TR13C_HUMAN	123-184	62	0	-	-

2.2b	ENST00000375887	2b	ENSE00001811977	chr13:108922066-108922582	517	TN13B_HUMAN	1-113	113	0	-	-
2.2e	ENST00000375887	2e	ENSE00000686291	chr13:108922688-108922772	85	TN13B_HUMAN	114-142	29	6	A:142-142 B:142-142 C:142-142 D:142-142 E:142-142 F:142-142	1 1 1 1 1 1
2.3	ENST00000375887	3	ENSE00000854068	chr13:108939151-108939207	57	TN13B_HUMAN	142-161	20	6	A:142-161 B:142-161 C:142-161 D:142-161 E:142-161 F:142-161	20 20 20 20 20 20
2.5a	ENST00000375887	5a	ENSE00000854071	chr13:108955601-108955713	113	TN13B_HUMAN	161-198	38	6	A:161-198 B:161-198 C:161-198 D:161-198 E:161-198 F:161-198	38 38 38 38 38 38
2.5c	ENST00000375887	5c	ENSE00000854073	chr13:108955802-108955952	151	TN13B_HUMAN	199-249	51	6	A:199-249 B:199-249 C:199-249 D:199-249 E:199-249 F:199-249	51 51 51 51 51 51
2.6c	ENST00000375887	6c	ENSE00001925016	chr13:108959174-108959385	212	TN13B_HUMAN	249-285	37	6	A:249-285 B:249-285 C:249-285 D:249-285 E:249-285 F:249-285	37 37 37 37 37 37

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:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56a_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee............ee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: A:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: A:161-198             Exon 2.5c  PDB: A:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: A:249-285             Transcript 2 (2)
                 3v56 A 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56b_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: B:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: B:161-198             Exon 2.5c  PDB: B:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: B:249-285             Transcript 2 (2)
                 3v56 B 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56c_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: C:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: C:161-198             Exon 2.5c  PDB: C:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: C:249-285             Transcript 2 (2)
                 3v56 C 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56d_ D: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee............ee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: D:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: D:161-198             Exon 2.5c  PDB: D:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: D:249-285             Transcript 2 (2)
                 3v56 D 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain E from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56e_ E: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: E:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: E:161-198             Exon 2.5c  PDB: E:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: E:249-285             Transcript 2 (2)
                 3v56 E 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain F from PDB  Type:PROTEIN  Length:144
 aligned with TN13B_HUMAN | Q9Y275 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:144
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281    
          TN13B_HUMAN   142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
               SCOP domains d3v56f_ F: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee......eee..eee..eeeeeee...eeee..eeee...eeeeeeeeeee.....ee..eeeee..........eeeeee..ee.......eeeeeeeeeee....eeeeee......ee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TNF_2  PDB: F:148-284 UniProt: 148-284                                                                                                   - PROSITE
           Transcript 2 (1) 2------------------Exon 2.5a  PDB: F:161-198             Exon 2.5c  PDB: F:199-249 UniProt: 199-249         ------------------------------------ Transcript 2 (1)
           Transcript 2 (2) Exon 2.3            ---------------------------------------------------------------------------------------Exon 2.6c  PDB: F:249-285             Transcript 2 (2)
                 3v56 F 142 VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL 285
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain G from PDB  Type:PROTEIN  Length:14
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:19
                                    27         
          TR13C_HUMAN    18 PCVPAECFDLLVRHCVACG  36
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
               Transcript 1 Exon 1.1            Transcript 1
                 3v56 G  22 xCH----WDLLVRHWV-Cx  35
                            | |    |27     | ||
                           22-ACE 25      33 ||
                             24             34|
                                             35-NH2

Chain H from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 H  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

Chain I from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 I  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

Chain J from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 J  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

Chain K from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 K  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

Chain L from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-.. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 L  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

Chain Z from PDB  Type:PROTEIN  Length:13
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:18
                                    28        
          TR13C_HUMAN    19 CVPAECFDLLVRHCVACG  36
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .e----ee....eee-e. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.1           Transcript 1
                 3v56 Z  23 CH----WDLLVRHWV-Cx  35
                             |    | 28    | ||
                             |   25      33 ||
                            24             34|
                                            35-NH2

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

)

Class: All beta proteins (24004)

Fold: TNF-like (100)

Superfamily: TNF-like (100)

Family: TNF-like (82)

Protein domain: automated matches (12)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d3v56a_	A:
1b	d3v56d_	D:
1c	d3v56e_	E:
1d	d3v56f_	F:
1e	d3v56b_	B:
1f	d3v56c_	C:

(no "CATH Domain" information available for 3V56)

(no "Pfam Domain" information available for 3V56)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (TN13B_HUMAN | Q9Y275)

molecular function
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0005164	tumor necrosis factor receptor binding	Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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: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:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving 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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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 G,H,I,J,K,L,Z (TR13C_HUMAN | Q96RJ3)

biological process
	GO:0031296	B cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B cell receptor to augment B cell activation.
	GO:0001782	B cell homeostasis	The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	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:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	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:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0002636	positive regulation of germinal center formation	Any process that activates or increases the frequency, rate, or extent of germinal center formation.
	GO:0045078	positive regulation of interferon-gamma biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
	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: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: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: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: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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3v56)

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	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
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Access by PDB/NDB ID
	3v56
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	TN13B_HUMAN \| Q9Y275
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TR13C_HUMAN \| Q96RJ3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	TN13B_HUMAN \| Q9Y275
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	TR13C_HUMAN \| Q96RJ3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TN13B_HUMAN \| Q9Y275	:	1jh5 1kd7 1kxg 1oqd 1oqe 1osg 4v46 4zch
	TR13C_HUMAN \| Q96RJ3	:	1mpv 1oqe 1osx 2hfg 4v46

1osg	THIS ENTRY 3V56 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1OSGSF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (2, 2)

SS Bonds (13, 13)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (6, 37)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (27, 33)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File