4JFY - 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 :   APO STRUCTURE OF PHOSPHOTYROSINE (PYAB) SCAFFOLD

Authors :   J. T. Koerber, N. D. Thomsen, B. T. Hannigan, W. F. Degrado, J. A. Wells

Date :   28 Feb 13 (Deposition) - 28 Aug 13 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.63

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: H,L  (1x)

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

Reference :   J. T. Koerber, N. D. Thomsen, B. T. Hannigan, W. F. Degrado, J. A. Wells
Nature-Inspired Design Of Motif-Specific Antibody Scaffolds
Nat. Biotechnol. V. 31 916 2013
PubMed-ID: 23955275 | Reference-DOI: 10.1038/NBT.2672

Molecule 1 - FAB LIGHT CHAIN
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C43 PRO+
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB HEAVY CHAIN
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C43 PRO+
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	PG4	4	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:9 , TYR A:87 , GLN A:100 , GLY A:101 , LYS A:103 , HOH A:406	BINDING SITE FOR RESIDUE PG4 A 301
2	AC2	SOFTWARE	TYR H:91 , PRO L:40 , GLY L:41	BINDING SITE FOR RESIDUE PG4 L 301
3	AC3	SOFTWARE	GLY H:42 , ALA L:9 , TYR L:87 , GLN L:100 , HOH L:418	BINDING SITE FOR RESIDUE PG4 L 302
4	AC4	SOFTWARE	LYS H:43 , GLY H:44 , GLU H:85 , GLN L:100	BINDING SITE FOR RESIDUE PG4 H 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	H:22	-	H:92
6	H:140	-	H:196
7	L:23	-	L:88

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Val 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 L:7	-	Pro L:8
7	Val L:94	-	Pro L:95
8	Tyr L:140	-	Pro L:141
9	Phe H:146	-	Pro H:147
10	Glu H:148	-	Pro H:149

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

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

(no "Exon" information available for 4JFY)

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:211
                                                                                                                                                                                                                                                    
               SCOP domains d4jfya1 A:1-107 automated matches                                                                          d4jfya2 A:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfy A    1 DIVLTQSPATLSLSPGERATLSCMTSTDIDDDMNWYQQKPGQAPRLLISEGNTLRPGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCLQSFNVPLTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfy B    1 EVQLVESGGGLVQPGGSLRLSCVTSGFTFRKFGMSWVRQAPGKGLEWVASIVTGGRKTYYSDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGYSSTSYAMDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123  ||   140       150       160       170       180       190       200       210    
                                                                              52A                            82A||               100A||                       126|                                                                                
                                                                                                              82B|                100B|                        134                                                                                
                                                                                                               82C                 100C

Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfy H   -1 ISEVQLVESGGGLVQPGGSLRLSCVTSGFTFRKFGMSWVRQAPGKGLEWVASIVTGGRKTYYSDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGYSSTSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                     8        18        28        38        48    |   57        67        77     |||84        94      |101       111       121       131       141       151       161       171       181       191       201       211     
                                                                                52A                            82A||               100A||                                                                                                                    
                                                                                                                82B|                100B|                                                                                                                    
                                                                                                                 82C                 100C

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4jfyl1 L:1-107 automated matches                                                                          d4jfyl2 L:108-213 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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jfy L    1 DIVLTQSPATLSLSPGERATLSCMTSTDIDDDMNWYQQKPGQAPRLLISEGNTLRPGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCLQSFNVPLTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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	d4jfya1	A:1-107
1b	d4jfyl1	L:1-107

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

Protein domain: automated matches (652)

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

2a	d4jfya2	A:108-211
2b	d4jfyl2	L:108-213

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

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

Asymmetric Unit(hide GO term definitions)

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

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val A:94 - Pro A:95	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

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

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	4jfy
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (7, 7)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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