2C1P - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   FAB-FRAGMENT OF ENANTIOSELECTIVE ANTIBODY COMPLEXED WITH FINROZOLE

Authors :   T. Parkkinen, T. K. Nevanen, A. Koivula, J. Rouvinen

Date :   19 Sep 05 (Deposition) - 25 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Fab Fragment, Enantioselective, Finrozole, Immune System, Antibody, Enantioselective Antibody, Immunoglobulin Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Parkkinen, T. K. Nevanen, A. Koivula, J. Rouvinen
Crystal Structures Of An Enantioselective Fab- Fragment In Free And Complex Forms.
J. Mol. Biol. V. 357 471 2006
PubMed-ID: 16427081 | Reference-DOI: 10.1016/J.JMB.2005.12.045

Molecule 1 - IGK-C PROTEIN
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	RV308
	Expression System Taxid	:	562
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	FINROZOLE-BINDING ANTIBODY

Molecule 2 - IGH-4 PROTEIN
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	RV308
	Expression System Taxid	:	562
	Fragment	:	FAB-FRAGMENT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	FINROZOLE-BINDING ANTIBODY

		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, 2)

No.	Name	Count	Type	Full Name
1	FNZ	2	Ligand/Ion	4-[(1S,2R)-3-(4-FLUOROPHENYL)-2-HYDROXY-1-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]BENZONITRILE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FNZ	1	Ligand/Ion	4-[(1S,2R)-3-(4-FLUOROPHENYL)-2-HYDROXY-1-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]BENZONITRILE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FNZ	1	Ligand/Ion	4-[(1S,2R)-3-(4-FLUOROPHENYL)-2-HYDROXY-1-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]BENZONITRILE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:36 , GLY A:91 , HIS A:93 , PHE A:94 , ASN B:35 , TRP B:47 , MET B:50 , ASP B:95 , TRP B:103 , HOH B:2056	BINDING SITE FOR RESIDUE FNZ B1215
2	AC2	SOFTWARE	LYS A:147 , TRP H:33 , ASN H:35 , TRP H:47 , MET H:50 , ASP H:95 , TRP H:103 , HOH H:2044 , HOH H:2094 , LEU L:36 , GLY L:91 , HIS L:93 , PHE L:94 , PRO L:96 , PHE L:98	BINDING SITE FOR RESIDUE FNZ H1214

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195
5	H:22	-	H:92
6	H:140	-	H:195
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Phe A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:146	-	Pro B:147
5	Ala B:148	-	Pro B:149
6	Trp B:188	-	Pro B:189
7	Phe H:146	-	Pro H:147
8	Ala H:148	-	Pro H:149
9	Trp H:188	-	Pro H:189
10	Ser L:7	-	Pro L:8
11	Phe L:94	-	Pro L:95
12	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 2C1P)

(no "PROSITE Motif" information available for 2C1P)

(no "Exon" information available for 2C1P)

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:218
 aligned with Q58EU8_MOUSE | Q58EU8 from UniProtKB/TrEMBL  Length:239

    Alignment length:218
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         Q58EU8_MOUSE    21 DVVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 238
               SCOP domains d2c1pa1 A:1-107 automated matches                                                                               d2c1pa2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains 2c1pA01 A:1-108 Immunoglobulins                                                                                  2c1pA02 A:109-213 Immunoglobulins                                                                         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
                 2c1p A   1 ELVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGSGSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c1pB01 B:2-113 Immunoglobulins                                                                                    2c1pB02 B:114-215 Immunoglobulins                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee....eeeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1p B   2 VQLQQSGAELVRPGTSVKLSCKASGYSFTNYWMNWLRQRPGQGLDWIGMIHPSDSETRLNQKFKDKATLTVDRSSSTAYIQLSSPTSEDSAVYYCARDDYDGAFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPAPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 215
                                    11        21        31        41        51 |      60        70        80  |||   87        97 ||    108       118       128       138       148       158       168       178       188       198       208       
                                                                             52A                            82A||               99|                                                                                                                  
                                                                                                             82B|               101                                                                                                                  
                                                                                                              82C

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2c1pH01 H:2-113 Immunoglobulins                                                                                    2c1pH02 H:114-214 Immunoglobulins                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee.....hhhh.eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1p H   2 VQLQQSGAELVRPGTSVKLSCKASGYSFTNYWMNWLRQRPGQGLDWIGMIHPSDSETRLNQKFKDKATLTVDRSSSTAYIQLSSPTSEDSAVYYCARDDYDGAFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPAPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 214
                                    11        21        31        41        51 |      60        70        80  |||   87        97 ||    108       118       128       138       148       158       168       178       188       198       208      
                                                                             52A                            82A||               99|                                                                                                                 
                                                                                                             82B|               101                                                                                                                 
                                                                                                              82C

Chain L from PDB  Type:PROTEIN  Length:217
 aligned with Q58EU8_MOUSE | Q58EU8 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q58EU8_MOUSE    22 VVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 238
               SCOP domains d2c1pl1 L:2-107 automated matches                                                                              d2c1pl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 2c1pL01 L:2-108 Immunoglobulins                                                                                 2c1pL02 L:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1p L   2 LVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGSGSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    11        21      |27D|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                    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(

)

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)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d2c1pa1	A:1-107
1b	d2c1pl1	L:2-107

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

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

2a	d2c1pa2	A:108-213
2b	d2c1pl2	L:108-213

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	2c1pA02	A:109-213
1b	2c1pL01	L:2-108
1c	2c1pA01	A:1-108
1d	2c1pB02	B:114-215
1e	2c1pH02	H:114-214
1f	2c1pB01	B:2-113
1g	2c1pH01	H:2-113
1h	2c1pL02	L:109-213

(no "Pfam Domain" information available for 2C1P)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2C1P)

Asymmetric Unit
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	Cis Peptide Bonds
		Ala B:148 - Pro B:149	[ RasMol ]
		Ala H:148 - Pro H:149	[ RasMol ]
		Phe A:94 - Pro A:95	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp B:188 - Pro B:189	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	2c1p
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	Q58EU8_MOUSE \| Q58EU8	:	1kn2 1kn4 1ncw 1nd0 1rua 1rum 1yei 1yej 1yek 2c1o

1afv	HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3
2c1o	ENAIIHIS FAB FRAGMENT IN THE FREE 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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