2C1O - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ENAIIHIS FAB FRAGMENT IN THE FREE FORM

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 :   2.75

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, Ena11His 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 Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	ENA11HIS 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 Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	ENA11HIS 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)

(no "Ligand,Modified Residues,Ions" information available for 2C1O)

(no "Site" information available for 2C1O)

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 2C1O)

(no "PROSITE Motif" information available for 2C1O)

(no "Exon" information available for 2C1O)

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:217
 aligned with Q58EU8_MOUSE | Q58EU8 from UniProtKB/TrEMBL  Length:239

    Alignment length:217
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q58EU8_MOUSE    21 DVVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 237
               SCOP domains d2c1oa1 A:1-107 automated matches                                                                               d2c1oa2 A:108-212 automated matches                                                                       SCOP domains
               CATH domains 2c1oA01 A:1-108 Immunoglobulins                                                                                  2c1oA02 A:109-212 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.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1o A   1 ELVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGSGSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c1oB01 B:1-113 Immunoglobulins                                                                                     2c1oB02 B:114-213 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
                 2c1o B   1 EVQLQQSGAELVRPGTSVKLSCKASGYSFTNYWMNWLRQRPGQGLDWIGMIHPSDSETRLNQKFKDKATLTVDRSSSTAYIQLSSPTSEDSAVYYCARDDYDGAFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPAPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 215
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127       137       147       157       167       177       187       197       207        
                                                                              52A                            82A||               99|                                                                                                                  
                                                                                                              82B|               101                                                                                                                  
                                                                                                               82C

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c1oH01 H:1-113 Immunoglobulins                                                                                     2c1oH02 H:114-213 Immunoglobulins                                                                   -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh....eeee....eeeeee........eeeeeeeee..eee....eeeee........eeeee.....hhhh.eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1o H   1 EVQLQQSGAELVRPGTSVKLSCKASGYSFTNYWMNWLRQRPGQGLDWIGMIHPSDSETRLNQKFKDKATLTVDRSSSTAYIQLSSPTSEDSAVYYCARDDYDGAFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPAPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 215
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127       137       147       157       167       177       187       197       207        
                                                                              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
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         Q58EU8_MOUSE    21 DVVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 237
               SCOP domains d2c1ol1 L:1-107 automated matches                                                                               d2c1ol2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 2c1oL01 L:1-108 Immunoglobulins                                                                                  2c1oL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee.......eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eee.........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1o L   1 ELVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLDSGDPDRFTGSGSGTDFTLKISRVEAEDLGIYYCVQGSHFPPTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    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(

)

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	d2c1oa1	A:1-107
1b	d2c1oa2	A:108-212
1c	d2c1ol1	L:1-107
1d	d2c1ol2	L:108-212

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mus musculus. Organism_taxid: 10090. (7)

1a	2c1oA02	A:109-212
1b	2c1oL02	L:109-212
1c	2c1oA01	A:1-108
1d	2c1oL01	L:1-108
1e	2c1oB02	B:114-213
1f	2c1oH02	H:114-213
1g	2c1oB01	B:1-113
1h	2c1oH01	H:1-113

(no "Pfam Domain" information available for 2C1O)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2C1O)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2c1o)

	Sites
(no "Sites" information available for 2c1o)

	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 ]

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

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

1afv	HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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