1YMH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ANTI-HCV FAB 19D9D6 COMPLEXED WITH PROTEIN L (PPL) MUTANT A66W

Authors :   V. Granata, N. G. Housden, S. Harrison, C. Jolivet-Reynaud, M. G. Gore,

Date :   21 Jan 05 (Deposition) - 31 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Engineering Of Crystal Contacts, Ppl-Fab Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Granata, N. G. Housden, S. Harrison, C. Jolivet-Reynaud, M. G. Gore E. A. Stura
Comparison Of The Crystallization And Crystal Packing Of Tw Fab Single-Site Mutant Protein L Complexes.
Acta Crystallogr. , Sect. D V. 61 750 2005
PubMed-ID: 15930633 | Reference-DOI: 10.1107/S0907444905007110

Molecule 1 - FAB 16D9D6, LIGHT CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	A, C
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - FAB 16D9D6, HEAVY CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	B, D
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - PROTEIN L
	Chains	:	E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	FINEGOLDIA MAGNA
	Organism Taxid	:	334413
	Strain	:	ATCC 29328
	Synonym	:	PPL

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B			E
Biological Unit 2 (1x)	:			C	D		F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YMH)

(no "Site" information available for 1YMH)

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	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:92
8	D:140	-	D:195

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Pro A:94	-	Pro A:95
3	Phe B:146	-	Pro B:147
4	Ser C:7	-	Pro C:8
5	Pro C:94	-	Pro C:95
6	Tyr C:140	-	Pro C:141
7	Phe D:146	-	Pro D:147

(no "SAP(SNP)/Variant" information available for 1YMH)

(no "PROSITE Motif" information available for 1YMH)

(no "Exon" information available for 1YMH)

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:220
                                                                                                                                                                                                                                                             
               SCOP domains d1ymha1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1ymha2 A:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ymhA01 A:1-108 Immunoglobulins                                                                                   1ymhA02 A:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh.....eeeeeeee........ee.........eeeee.........eeeeeee..hhhhhh.....eeee........eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ymh A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKVLIYWASTRESGVPDRFTGRGSGTDFTLTISSVQAEDQAVYYCKQAYIPPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
                                                     27A|||||                                                                                                                                                                                           
                                                      27B||||                                                                                                                                                                                           
                                                       27C|||                                                                                                                                                                                           
                                                        27D||                                                                                                                                                                                           
                                                         27E|                                                                                                                                                                                           
                                                          27F

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1ymhb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d1ymhb2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1ymhB01 B:1-113 Immunoglobulins                                                                                       1ymhB02 B:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee.........eeee..........eeeeeeeeeee.....eeee.hhh....eee.........eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ymh B    1 QIQLVQSGPELKKPGETVKISCKASGYTFTDFSMHWVNQAPGKGLNWMGWVNTETGEPTYADDFKGRFAFSLETSASTAYLQINSLKNEDTATYFCARFLLRQYFDVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A                            82A||               100A                                                                                                                 
                                                                                                              82B|                                                                                                                                    
                                                                                                               82C

Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains d1ymhc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1ymhc2 C:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ymhC01 C:1-108 Immunoglobulins                                                                                   1ymhC02 C:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeee.......eee...........ee...............eeeeeeehhhhhh..eeeeeee........eeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ymh C    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKVLIYWASTRESGVPDRFTGRGSGTDFTLTISSVQAEDQAVYYCKQAYIPPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
                                                     27A|||||                                                                                                                                                                                           
                                                      27B||||                                                                                                                                                                                           
                                                       27C|||                                                                                                                                                                                           
                                                        27D||                                                                                                                                                                                           
                                                         27E|                                                                                                                                                                                           
                                                          27F

Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1ymhd1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                        d1ymhd2 D:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1ymhD01 D:1-113 Immunoglobulins                                                                                       1ymhD02 D:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee...........eeeeeeeeee.....eeee........eee...eee..eeeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ymh D    1 QIQLVQSGPELKKPGETVKISCKASGYTFTDFSMHWVNQAPGKGLNWMGWVNTETGEPTYADDFKGRFAFSLETSASTAYLQINSLKNEDTATYFCARFLLRQYFDVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A                            82A||               100A                                                                                                                 
                                                                                                              82B|                                                                                                                                    
                                                                                                               82C

Chain E from PDB  Type:PROTEIN  Length:65
 aligned with Q51918_FINMA | Q51918 from UniProtKB/TrEMBL  Length:992

    Alignment length:65
                                   483       493       503       513       523       533     
        Q51918_FINMA    474 KEEVTIKVNLIFADGKTQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGYTINIKFAGK  538
               SCOP domains d1ymhe_ E: automated matches                                      SCOP domains
               CATH domains 1ymhE00 E:818-882  [code=3.10.20.10, no name defined]             CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                1ymh E  818 KEEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTWDLEDGGNHMNIKFAGK  882
                                   827       837       847       857       867       877

Chain F from PDB  Type:PROTEIN  Length:65
 aligned with Q51918_FINMA | Q51918 from UniProtKB/TrEMBL  Length:992

    Alignment length:65
                                   483       493       503       513       523       533     
        Q51918_FINMA    474 KEEVTIKVNLIFADGKTQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGYTINIKFAGK  538
               SCOP domains d1ymhf_ F: automated matches                                      SCOP domains
               CATH domains 1ymhF00 F:818-882  [code=3.10.20.10, no name defined]             CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eee..ee.hhhhhhhhhhhhhhhhhh....ee........ee..ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                1ymh F  818 KEEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTWDLEDGGNHMNIKFAGK  882
                                   827       837       847       857       867       877

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: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.10, no name defined] (72)

House mouse (Mus musculus) (6)

1a	1ymhE00	E:818-882
1b	1ymhF00	F:818-882

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1ymhA02	A:109-211
2b	1ymhB02	B:114-212
2c	1ymhD02	D:114-212
2d	1ymhA01	A:1-108
2e	1ymhC01	C:1-108
2f	1ymhB01	B:1-113
2g	1ymhD01	D:1-113
2h	1ymhC02	C:109-211

(no "Pfam Domain" information available for 1YMH)

Asymmetric Unit(hide GO term definitions)

Chain E,F (Q51918_FINMA | Q51918)

biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ymh)

	Sites
(no "Sites" information available for 1ymh)

	Cis Peptide Bonds
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe D:146 - Pro D:147	[ RasMol ]
		Pro A:94 - Pro A:95	[ RasMol ]
		Pro C:94 - Pro C:95	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]

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

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	1ymh
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	Q51918_FINMA \| Q51918
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	Q51918_FINMA \| Q51918	:	1hez 1ynt 2fs1 4hjg 4hkz 4ioi

(no "Related Entries Specified in the PDB File" available for 1YMH)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (7, 7)

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