5VCN - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 5H8

Authors :   T. Osinski, K. A. Majorek, A. Pomes, L. R. Offermann, S. Osinski, J. Gles L. D. Vailes, M. D. Chapman, W. Minor, M. Chruszcz

Date :   31 Mar 17 (Deposition) - 26 Apr 17 (Release) - 03 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Allergen, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Osinski, A. Pomes, K. A. Majorek, J. Glesner, L. R. Offermann, L. D. Vailes, M. D. Chapman, W. Minor, M. Chruszcz
Structural Analysis Of Der P 1-Antibody Complexes And Comparison With Complexes Of Proteins Or Peptides With Monoclonal Antibodies.
J. Immunol. V. 195 307 2015
PubMed-ID: 26026055 | Reference-DOI: 10.4049/JIMMUNOL.1402199

Molecule 1 - PEPTIDASE 1
	Chains	:	A, B
	Organism Common	:	EUROPEAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES PTERONYSSINUS
	Organism Taxid	:	6956
	Synonym	:	ALLERGEN DER P I, MAJOR MITE FECAL ALLERGEN DER P 1

Molecule 2 - LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
	Chains	:	C, E
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	HYBRIDOMA
	Expression System Taxid	:	10090
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
	Chains	:	D, F
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	HYBRIDOMA
	Expression System Taxid	:	10090
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:44 , ASP A:56 , LEU A:57 , GLU A:59 , GLU A:91	binding site for residue CA A 301
2	AC2	SOFTWARE	GLY A:155 , TYR A:203	binding site for residue PO4 A 302
3	AC3	SOFTWARE	THR A:1 , GLN A:118	binding site for residue EDO A 303
4	AC4	SOFTWARE	GLU B:44 , ASP B:56 , LEU B:57 , GLU B:59 , GLU B:91	binding site for residue CA B 301
5	AC5	SOFTWARE	TYR B:203	binding site for residue PO4 B 302
6	AC6	SOFTWARE	THR B:1 , GLN B:118	binding site for residue EDO B 303
7	AC7	SOFTWARE	ASN A:52	binding site for Mono-Saccharide NAG A 304 bound to ASN A 52
8	AC8	SOFTWARE	ASN B:52	binding site for Mono-Saccharide NAG B 304 bound to ASN B 52

Asymmetric Unit

No.	Residues
1	A:4	-	A:117
2	A:31	-	A:71
3	A:65	-	A:103
4	B:4	-	B:117
5	B:31	-	B:71
6	B:65	-	B:103
7	C:23	-	C:88
8	C:133	-	C:193
9	D:22	-	D:95
10	D:147	-	D:202
11	E:23	-	E:88
12	E:133	-	E:193
13	F:22	-	F:95
14	F:147	-	F:202

Asymmetric Unit

No.	Residues
1	Tyr A:120	-	Pro A:121
2	Tyr B:120	-	Pro B:121
3	Tyr C:139	-	Pro C:140
4	Phe D:153	-	Pro D:154
5	Glu D:155	-	Pro D:156
6	Trp D:195	-	Pro D:196
7	Tyr E:139	-	Pro E:140
8	Phe F:153	-	Pro F:154
9	Glu F:155	-	Pro F:156
10	Trp F:195	-	Pro F:196

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

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

(no "Exon" information available for 5VCN)

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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhhh..............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vcn A   1 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vcn B   1 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee.........eeeeee.....ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vcn C   1 DIQMTQTTSSLSASLGDRVTISCRASQDITNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGKTLPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeee..........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vcn D   1 EVQLVESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGRIDYNLVRKSRLSISKDNSQSQIFLKMNSLQTDDTARYYCARAYQRYDYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  147       157       167       177       187       197       207       217   
                                                                                                                                                               134|                                                                              
                                                                                                                                                                142

Chain E from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee.........eeeeee.....ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vcn E   1 DIQMTQTTSSLSASLGDRVTISCRASQDITNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGKTLPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee.....eeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeee..........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vcn F   1 EVQLVESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGRIDYNLVRKSRLSISKDNSQSQIFLKMNSLQTDDTARYYCARAYQRYDYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 146       156       166       176       186       196       206       216    
                                                                                                                                                                135|                                                                              
                                                                                                                                                                 142

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 5VCN)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Glu D:155 - Pro D:156	[ RasMol ]
		Glu F:155 - Pro F:156	[ RasMol ]
		Phe D:153 - Pro D:154	[ RasMol ]
		Phe F:153 - Pro F:154	[ RasMol ]
		Trp D:195 - Pro D:196	[ RasMol ]
		Trp F:195 - Pro F:196	[ RasMol ]
		Tyr A:120 - Pro A:121	[ RasMol ]
		Tyr B:120 - Pro B:121	[ RasMol ]
		Tyr C:139 - Pro C:140	[ RasMol ]
		Tyr E:139 - Pro E:140	[ RasMol ]

Biological Units
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	5vcn
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	Q3HWZ5_DERPT \| Q3HWZ5
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		Domain Information	:	XDom
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	Q3HWZ5_DERPT \| Q3HWZ5	:	5vco 5vpg
UniProtKB/TrEMBL
	Q3HWZ5_DERPT \| Q3HWZ5	:	3f5v

3rvv	ALMOST THE SAME PROTEIN, DIFFERENT ANTIBODY
3rvw	THE SAME PROTEIN, DIFFERENT ANTIBODY
3rvx	THE SAME PROTEIN, DIFFERENT ANTIBODY
4poz	THE SAME PROTEIN BUT WITHOUT ALLERGEN
4pp2	THE SAME PROTEIN, DIFFERENT ANTIBODY
5vco

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (14, 14)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (5, 5)

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Related Entries

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Related Entries Specified in the PDB File