4HIH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND RHAMNOSE.

Authors :   S. Bryson, L. Risnes, S Damgupta, C. A. Thomson, J. W. Schrader, E. F. Pa

Date :   11 Oct 12 (Deposition) - 28 Aug 13 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Immunoglobin, Antibody, Streptococcus Pneumoniae 23F, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bryson, L. Risnes, S Damgupta, C. A. Thomson, J. W. Schrader, E. F. Pai
Multitasking Immunoglobulin V-Genes And Somatic Diversity I Cdr3 Loops Generate Binding Sites For Chemically Distinct Antigens From Bacterial And Viral Pathogens
To Be Published
PubMed: search

Molecule 1 - FAB 023.102
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PARC
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - ANTIBODY 023.102
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PARC
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	RAM	2	Ligand/Ion	ALPHA-L-RHAMNOSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	RAM	1	Ligand/Ion	ALPHA-L-RHAMNOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	RAM	1	Ligand/Ion	ALPHA-L-RHAMNOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:91 , ASN A:93 , TRP A:94 , GLY B:33 , GLU B:95 , HOH B:317	BINDING SITE FOR RESIDUE RAM A 301
2	AC2	SOFTWARE	ARG C:91 , ASP C:92 , ASN C:93 , TRP C:94 , PRO C:95A , GLY D:33 , GLU D:95 , LYS D:100 , HOH D:408 , HOH D:465	BINDING SITE FOR RESIDUE RAM D 301

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:196
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:92
8	D:140	-	D:196

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Trp A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:146	-	Pro B:147
5	Glu B:148	-	Pro B:149
6	Ser C:7	-	Pro C:8
7	Trp C:94	-	Pro C:95
8	Tyr C:140	-	Pro C:141
9	Phe D:146	-	Pro D:147
10	Glu D:148	-	Pro D:149

(no "SAP(SNP)/Variant" information available for 4HIH)

(no "PROSITE Motif" information available for 4HIH)

(no "Exon" information available for 4HIH)

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:212
                                                                                                                                                                                                                                                     
               SCOP domains d4hiha1 A:2-107 automated matches                                                                           d4hiha2 A:108-211 automated matches                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeee......eee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hih A    2 GQLTQSPATLSLSPGERATLSCRASQSVTNYLAWYQQKPGQAPRLLIYGASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRDNWPPDATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNR  211
                                    11        21        31        41        51        61        71        81        91    ||  99       109       119       129       139       149       159       169       179       189       199       209  
                                                                                                                        95A|                                                                                                                    
                                                                                                                         95B

Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..eeeeeeehhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hih B    1 LINLVESGGGVVQPGRSLRLSCAASGFTFSRYGMHWVRQAPGKGLEWVAVVSSDGRTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVFYCAKEGGDNKFSFDYWGQGTLVTVSSASTKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVQTYTCNVDHKPSNTKVDKTVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123 ||    142       152       162       172       182 ||    199       209   
                                                                              52A                            82A||               100A||                      125|                                              184|                    
                                                                                                              82B|                100B|                       135                                               192                    
                                                                                                               82C                 100C

Chain C from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d4hihc1 C:2-107 automated matches                                                                       d4hihc2 C:108-211 automated matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee.....eeeeee....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hih C    2 GQLTQSPATLSLSPGERATLSCRATNYLAWYQQKPGQAPRLLIYGASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRDNWPPDATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNR  211
                                    11        21   ||   35        45        55        65        75        85        95||     103       113       123       133       143       153       163       173       183       193       203        
                                                  25|                                                               95A|                                                                                                                    
                                                   30                                                                95B

Chain D from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee...eeeeeeeee.....eeee........eee...ee.....eeeeeeee....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hih D    1 LINLVESGGGVVQPGRSLRLSCAASGFTFSRYGMHWVRQAPGKGLEWVAVVSSDGRTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVFYCAKEGGDNKFSFDYWGQGTLVTVSSASTKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVQTYTCNVDHKPSNTKVDKTVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123 ||    142       152       162       172       182 ||    199       209   
                                                                              52A                            82A||               100A||                      125|                                              184|                    
                                                                                                              82B|                100B|                       135                                               192                    
                                                                                                               82C                 100C

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(

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Superfamilies( (-)

)

Families(

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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	d4hiha1	A:2-107
1b	d4hiha2	A:108-211
1c	d4hihc1	C:2-107
1d	d4hihc2	C:108-211

(no "CATH Domain" information available for 4HIH)

(no "Pfam Domain" information available for 4HIH)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4HIH)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu D:148 - Pro D:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe D:146 - Pro D:147	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Trp A:94 - Pro A:95	[ RasMol ]
		Trp C:94 - Pro C:95	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4hih
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4hh9	ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5
4hha	ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5 WITH EPITOPE PEPTIDE AD-2S1
4hie	ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102
4hii	ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND RHAMNOSE-GALACTOSE
4hij	ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND L- RHAMNOSE-(1-2)-ALPHA-D-GALACTOSE-(3-O)-PHOSPHATE-2-GLYCEROL

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

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