3FO9 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ALDOLASE ANTIBODY 33F12 FAB' IN COMPLEX WITH HAPTEN 1,3-DIKETONE

Authors :   X. Zhu, I. A. Wilson

Date :   29 Dec 08 (Deposition) - 22 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Aldolase Antibody, Enamine Intermediate, Amine Catalysis, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhu, F. Tanaka, R. A. Lerner, C. F. Barbas, I. A. Wilson
Direct Observation Of An Enamine Intermediate In Amine Catalysis
J. Am. Chem. Soc. V. 131 18206 2009
PubMed-ID: 19968282 | Reference-DOI: 10.1021/JA907271A

Molecule 1 - IMMUNOGLOBULIN IGG2A - LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Fragment	:	LIGHT CHAIN OF 33F12 FAB' FRAGMENT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IMMUNOGLOBULIN IGG2A - HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Fragment	:	HEAVY CHAIN OF 33F12 FAB' FRAGMENT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	DIK	2	Ligand/Ion	5-{[4-(5-METHYL-3-OXOHEX-4-EN-1-YL)PHENYL]AMINO}-5-OXOPENTANOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DIK	1	Ligand/Ion	5-{[4-(5-METHYL-3-OXOHEX-4-EN-1-YL)PHENYL]AMINO}-5-OXOPENTANOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DIK	1	Ligand/Ion	5-{[4-(5-METHYL-3-OXOHEX-4-EN-1-YL)PHENYL]AMINO}-5-OXOPENTANOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP H:33 , LYS H:93 , TYR H:95 , PHE H:96 , TYR H:97 , TRP H:103 , HIS L:27D , ASN L:34 , TYR L:36 , SER L:89 , GLY L:91 , PHE L:98 , HOH L:280	BINDING SITE FOR RESIDUE DIK H 500
2	AC2	SOFTWARE	TYR A:36 , SER A:89 , GLY A:91 , PHE A:98 , TRP B:33 , LYS B:93 , TYR B:95 , PHE B:96 , TYR B:97 , TRP B:103 , HOH L:299 , HOH L:306 , HOH L:437	BINDING SITE FOR RESIDUE DIK B 500

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:208
5	H:22	-	H:92
6	H:142	-	H:208
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Val L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:148	-	Pro H:149
5	Glu H:150	-	Pro H:151
6	Trp H:199	-	Pro H:200
7	Thr A:7	-	Pro A:8
8	Val A:94	-	Pro A:95
9	Tyr A:140	-	Pro A:141
10	Phe B:148	-	Pro B:149
11	Glu B:150	-	Pro B:151
12	Trp B:199	-	Pro B:200

(no "SAP(SNP)/Variant" information available for 3FO9)

(no "PROSITE Motif" information available for 3FO9)

(no "Exon" information available for 3FO9)

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:219
                                                                                                                                                                                                                                                           
               SCOP domains d3fo9a1 A:1-107 automated matches                                                                               d3fo9a2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo9A02 A:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....eee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo9 A   1 ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSYGNTFLNWYLQKSGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                                                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d3fo9b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d3fo9b2 B:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 3fo9B01 B:1-113 Immunoglobulins                                                                                       3fo9B02 B:114-227 Immunoglobulins                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo9 B   1 EVKLEESGGGLVQPGGSMKLSCVVSGLTFSRFWMSWVRQSPEKGLEWVAEIRLKSDNYATHYAESVKGKFTISRDDSKSRLYLQMNSLRTEDTGIYYCKIYFYSFSYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30        40        50  |||   57        67        77     |||84        94     ||105       115       125    || 137       147      |162      |173      |185       195|| ||  208       218    ||  
                                                                              52A||                            82A||               100|                         130|                  154|||    169|      180|          196| || 206|            223|  
                                                                               52B|                             82B|                102                          133                   156||     171       183           198 ||  208             226  
                                                                                52C                              82C                                                                    157|                               200|                       
                                                                                                                                                                                         162                                202

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d3fo9h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d3fo9h2 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 3fo9H01 H:1-113 Immunoglobulins                                                                                       3fo9H02 H:114-227 Immunoglobulins                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee.hhhhh..eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo9 H   1 EVKLEESGGGLVQPGGSMKLSCVVSGLTFSRFWMSWVRQSPEKGLEWVAEIRLKSDNYATHYAESVKGKFTISRDDSKSRLYLQMNSLRTEDTGIYYCKIYFYSFSYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    10        20        30        40        50  |||   57        67        77     |||84        94     ||105       115       125    || 137       147      |162      |173      |185       195|| ||  208       218    ||  
                                                                              52A||                            82A||               100|                         130|                  154|||    169|      180|          196| || 206|            223|  
                                                                               52B|                             82B|                102                          133                   156||     171       183           198 ||  208             226  
                                                                                52C                              82C                                                                    157|                               200|                       
                                                                                                                                                                                         162                                202

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3fo9l1 L:1-107 automated matches                                                                               d3fo9l2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3fo9L02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....eee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fo9 L   1 ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSYGNTFLNWYLQKSGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQGTHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                                                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	3fo9A02	A:109-214
1b	3fo9B02	B:114-227
1c	3fo9H02	H:114-227
1d	3fo9B01	B:1-113
1e	3fo9H01	H:1-113
1f	3fo9L02	L:109-214

(no "Pfam Domain" information available for 3FO9)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:150 - Pro B:151	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp B:199 - Pro B:200	[ RasMol ]
		Trp H:199 - Pro H:200	[ 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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1axt	THE SAME PROTEIN IN APO-FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 8)

CATH Domains (1, 6)

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Gene Ontology (29, 29)

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