5DMJ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB

Authors :   S. Sheriff

Date :   08 Sep 15 (Deposition) - 01 Jun 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.79

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

Keywords :   Cell Surface Receptor, Domain Antibody, Protein/Protein Interaction, Immune System-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Yamniuk, A. Suri, S. R. Krystek, J. Tamura, V. Ramamurthy, R. Kuhn K. Carroll, C. Fleener, R. Ryseck, L. Cheng, Y. An, P. Drew, S. Grant, S. J. Suchard, S. G. Nadler, J. W. Bryson, S. Sheriff
Functional Antagonism Of Human Cd40 Achieved By Targeting A Unique Species-Specific Epitope.
J. Mol. Biol. V. 428 2860 2016
PubMed-ID: 27216500 | Reference-DOI: 10.1016/J.JMB.2016.05.014

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 5
	Chains	:	A, D, F
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Gene	:	CD40, TNFRSF5
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	B-CELL SURFACE ANTIGEN CD40,BP50,CD40L RECEPTOR,CDW40

Molecule 2 - 3H65-5 DOMAIN ANTIBODY (DAB)
	Chains	:	B, E, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDOM13
	Expression System Strain	:	HB2151
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	K	3	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:125 , SER A:126 , PHE A:129 , SER A:152 , ASP A:153 , VAL A:154 , HOH A:401	binding site for residue K A 301
2	AC2	SOFTWARE	CYS D:125 , SER D:126 , PHE D:129 , SER D:152 , VAL D:154 , HOH D:403	binding site for residue K D 301
3	AC3	SOFTWARE	CYS F:125 , SER F:126 , PHE F:129 , SER F:152 , VAL F:154	binding site for residue K F 301

Asymmetric Unit

No.	Residues
1	A:26	-	A:37
2	A:38	-	A:51
3	A:41	-	A:59
4	A:62	-	A:77
5	A:83	-	A:103
6	A:105	-	A:119
7	A:111	-	A:116
8	A:125	-	A:143
9	A:146	-	A:161
10	A:167	-	A:186
11	B:22	-	B:92
12	D:26	-	D:37
13	D:38	-	D:51
14	D:41	-	D:59
15	D:62	-	D:77
16	D:83	-	D:103
17	D:105	-	D:119
18	D:111	-	D:116
19	D:125	-	D:143
20	D:146	-	D:161
21	D:167	-	D:186
22	E:22	-	E:92
23	F:26	-	F:37
24	F:38	-	F:51
25	F:41	-	F:59
26	F:62	-	F:77
27	F:83	-	F:103
28	F:105	-	F:119
29	F:111	-	F:116
30	F:125	-	F:143
31	F:146	-	F:161
32	F:167	-	F:186
33	G:22	-	G:92

Asymmetric Unit

No.	Residues
1	Glu A:107	-	Gly A:108
2	Leu B:95	-	Pro B:96
3	Asn D:34	-	Ser D:35
4	Ala D:115	-	Cys D:116
5	Gly D:128	-	Phe D:129
6	Glu D:159	-	Lys D:160
7	Leu E:95	-	Pro E:96
8	Ala F:115	-	Cys F:116
9	Gly F:128	-	Phe F:129
10	Thr F:136	-	Gly F:137
11	Leu G:95	-	Pro G:96

(no "SAP(SNP)/Variant" information available for 5DMJ)

(no "PROSITE Motif" information available for 5DMJ)

(no "Exon" information available for 5DMJ)

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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeee........eeee....ee..........ee....hhhh.eeeee........eeee....ee.......ee.........ee...........ee.....ee..........ee......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj A  24 TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGP 188
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...........eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj B   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFRDYEMWWVRQAPGKGLERVSAINPQGTRTYYADSVMGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLPFTFDDWGQGTLVTVSSA 114
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       
                                                                              52A                            82A||               99|             
                                                                                                              82B|               101             
                                                                                                               82C

Chain D from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeee........eeee....ee..........ee....hhhh.eeeee........eeee....ee.......ee.........eeeee......eeee.....ee..........ee..........eee........ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj D  24 TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGPQD 190
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

Chain E from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj E  -1 TEVQLLESGGGLVQPGGSLRLSCAASGFTFRDYEMWWVRQAPGKGLERVSAINPQGTRTYYADSVMGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLPFTFDDWGQGTLVTVS 112
                            ||       9        19        29        39        49   |    58        68        78    ||| 85        95   ||  106      
                           -1|                                                 52A                            82A||               99|           
                             1                                                                                 82B|               101           
                                                                                                                82C

Chain F from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee.............ee....ee..........ee....hhhh.eeeee........eeee....ee.......ee.........ee...........ee.....ee..........ee...hhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj F  26 CREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGP 188
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185

Chain G from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmj G   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFRDYEMWWVRQAPGKGLERVSAINPQGTRTYYADSVMGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLPFTFDDWGQGTLVTVSS 113
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107      
                                                                              52A                            82A||               99|            
                                                                                                              82B|               101            
                                                                                                               82C

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 '\|'

(no "SCOP Domain" information available for 5DMJ)

(no "CATH Domain" information available for 5DMJ)

(no "Pfam Domain" information available for 5DMJ)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala D:115 - Cys D:116	[ RasMol ]
		Ala F:115 - Cys F:116	[ RasMol ]
		Asn D:34 - Ser D:35	[ RasMol ]
		Glu A:107 - Gly A:108	[ RasMol ]
		Glu D:159 - Lys D:160	[ RasMol ]
		Gly D:128 - Phe D:129	[ RasMol ]
		Gly F:128 - Phe F:129	[ RasMol ]
		Leu B:95 - Pro B:96	[ RasMol ]
		Leu E:95 - Pro E:96	[ RasMol ]
		Leu G:95 - Pro G:96	[ RasMol ]
		Thr F:136 - Gly F:137	[ RasMol ]

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	TNR5_HUMAN \| P25942	:	1cdf 1czz 1d00 1fll 1lb6 3qd6 5dmi 5ihl

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (33, 33)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (51, 51)

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