4HH9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5

Authors :   S. Bryson, L. Risnes, S. Damgupta, C. A. Thomson, R. Pfoh, J. W. Schrader

Date :   09 Oct 12 (Deposition) - 23 Oct 13 (Release) - 23 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Fab, Antibody, 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 KE5, LIGHT CHAIN
	Chains	:	A, C
	Fragment	:	KE5 LIGHT CHAIN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB KE5, HEAVY CHAIN
	Chains	:	B, D
	Fragment	:	KE5 HEAVY CHAIN
	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)

(no "Ligand,Modified Residues,Ions" information available for 4HH9)

(no "Site" information available for 4HH9)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	A:214	-	B:216
4	B:22	-	B:92
5	B:140	-	B:196
6	C:23	-	C:88
7	C:134	-	C:194
8	C:214	-	D:216
9	D:22	-	D:92
10	D:140	-	D:196

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4HH9)

(no "PROSITE Motif" information available for 4HH9)

(no "Exon" information available for 4HH9)

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:214
                                                                                                                                                                                                                                                       
               SCOP domains d4hh9a1 A:1-107 automated matches                                                                           d4hh9a2 A:108-214 automated matches                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeeee.......eeeee..hhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hh9 A    1 EVVLTQSPATLSLSPGERATISCRASQSVGGYLTWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISGLEPEDFAIYYCQQRGNWPPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90     |  99       109       119      |130       140       150       160       170       180       190       200       210    
                                                                                                                         95A                            126|                                                                                      
                                                                                                                                                         128

Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hh9 B    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSNHGMHWVRQAPGKRLEWVAVISYDGRHEHYADLVKGRFTISRDNSKNTLYLQMNSLRAEDRALYFCAREGLSRDNSGFTGLIDYWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD  217
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208         
                                                                              52A                            82A||               100A|||||||                                                                                                                     
                                                                                                              82B|                100B||||||                                                                                                                     
                                                                                                               82C                 100C|||||                                                                                                                     
                                                                                                                                    100D||||                                                                                                                     
                                                                                                                                     100E|||                                                                                                                     
                                                                                                                                      100F||                                                                                                                     
                                                                                                                                       100G|                                                                                                                     
                                                                                                                                        100H

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4hh9c1 C:1-107 automated matches                                                                           d4hh9c2 C:108-214 automated matches                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.......ee...eeeee.......eeeee.........eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hh9 C    1 EVVLTQSPATLSLSPGERATISCRASQSVGGYLTWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISGLEPEDFAIYYCQQRGNWPPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90     |  99       109       119      |130       140       150       160       170       180       190       200       210    
                                                                                                                         95A                            126|                                                                                      
                                                                                                                                                         128

Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               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..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4hh9 D    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSNHGMHWVRQAPGKRLEWVAVISYDGRHEHYADLVKGRFTISRDNSKNTLYLQMNSLRAEDRALYFCAREGLSRDNSGFTGLIDYWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208        
                                                                              52A                            82A||               100A|||||||                                                                                                                    
                                                                                                              82B|                100B||||||                                                                                                                    
                                                                                                               82C                 100C|||||                                                                                                                    
                                                                                                                                    100D||||                                                                                                                    
                                                                                                                                     100E|||                                                                                                                    
                                                                                                                                      100F||                                                                                                                    
                                                                                                                                       100G|                                                                                                                    
                                                                                                                                        100H

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	d4hh9a1	A:1-107
1b	d4hh9c1	C:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

2a	d4hh9a2	A:108-214
2b	d4hh9c2	C:108-214

(no "CATH Domain" information available for 4HH9)

(no "Pfam Domain" information available for 4HH9)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4HH9)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4hh9)

	Sites
(no "Sites" information available for 4hh9)

	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 ]
		Pro A:95 - Pro A:95A	[ RasMol ]
		Pro C:95 - Pro C:95A	[ 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
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4hh9
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4hha	ANTI-HUMAN CYTOMEGALOVIRUS (HCMV) FAB KE5 WITH EPITOPE PEPTIDE AD-2S1
4hie	ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102
4hih	ANTI-STREPTOCOCCUS PNEUMONIAE 23F FAB 023.102 WITH BOUND RHAMNOSE
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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Structural Features

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 4)

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