3LHP - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HIV EPITOPE-SCAFFOLD 4E10_D0_1ISEA_004_N 4E10 FV COMPLEX

Authors :   M. A. Holmes

Date :   22 Jan 10 (Deposition) - 22 Sep 10 (Release) - 22 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : H,I,L,M,S,T
Biol. Unit 1: H,L,S  (1x)
Biol. Unit 2: I,M,T  (1x)

Keywords :   Epitope-Scaffold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. E. Correia, Y. E. Ban, M. A. Holmes, H. Xu, K. Ellingson, Z. Kraft, C. Carrico, E. Boni, D. N. Sather, C. Zenobia, K. Y. Burke, T. Bradley-Hewitt, J. F. Bruhn-Johannsen, O. Kalyuzhniy, D. Baker, R. K. Strong, L. Stamatatos, W. R. Schief
Computational Design Of Epitope-Scaffolds Allows Induction Of Antibodies Specific For A Poorly Immunogenic Hiv Vaccine Epitope.
Structure V. 18 1116 2010
PubMed-ID: 20826338 | Reference-DOI: 10.1016/J.STR.2010.06.010

Molecule 1 - FV 4E10 HEAVY CHAIN
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FV 4E10 LIGHT CHAIN
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - 4E10_D0_1ISEA_004_N (T93)
	Chains	:	S, T
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29
	Expression System Strain	:	BL21(DE3) STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARTIFICIAL GENE
	Organism Taxid	:	32630
	Other Details	:	THE EPITOPE-SCAFFOLD IS BASED ON A MUTANT OF RIBOSOME RECYCLING FACTOR FROM ESCHERICHIA COLI (PDB ID 1ISE)

		1	2	3	4	5	6
Asymmetric Unit	:	H	I	L	M	S	T
Biological Unit 1 (1x)	:	H		L		S
Biological Unit 2 (1x)	:		I		M		T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN M:38 , LEU M:48 , ALA M:60 , PHE M:63	BINDING SITE FOR RESIDUE EDO M 113

Asymmetric Unit

No.	Residues
1	H:22	-	H:96
2	I:22	-	I:96
3	L:23	-	L:89
4	M:23	-	M:89

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Ser M:7	-	Pro M:8

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

(no "PROSITE Motif" information available for 3LHP)

(no "Exon" information available for 3LHP)

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 H from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d3lhph_ H: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeeeee.....eeeeeeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp H   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGLGKPIGAFAHWGQGTLVTVSSL 128
                                    11        21        31        41        51        61        71        81        91       101 ||    114       124    
                                                                                                                               103|                     
                                                                                                                                107

Chain I from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d3lhpi_ I: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..............ee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp I   2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGLGKPIGAFAHWGQGTLVTVS 126
                                    11        21        31        41        51        61        71        81        91       101 ||    114       124  
                                                                                                                               103|                   
                                                                                                                                107

Chain L from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains d3lhpl_ L: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp L   1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKLVP 111
                                    10        20        30        40        50        60        70        80        90       100       110

Chain M from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d3lhpm_ M: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee.....eeeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp M   1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKLV 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain S from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp S   7 GSISDIRKDAEVRMDKAVEAFKNKLDKFKAAVRKVFPTEERIKDWLKIVRGEAEQARVAVRNVGRDANDKAAALGKDKEINWFDISQSLWDVQKLTDAAIKKIEAALADMEAWLTQ 122
                                    16        26        36        46        56        66        76        86        96       106       116

Chain T from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 3lhp T  11 DIRKDAEVRMDKAVEAFKNKLDKFKAAVRKVFPTEERIKDWLKIVRGEAEQARVAVRNVGRNDKAAALGKDKEINWFDISQSLWDVQKLTDAAIKKIEAALADMEAWLTQ 122
                                    20        30        40        50        60        70||      82        92       102       112       122
                                                                                       71|                                                
                                                                                        74

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

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

1a	d3lhph_	H:
1b	d3lhpi_	I:
1c	d3lhpl_	L:
1d	d3lhpm_	M:

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

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

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3LHP)

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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	3lhp
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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