1YUH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FAB FRAGMENT

Authors :   S. C. Yuhasz, L. M. Amzel, C. Parry, M. Strand

Date :   30 Jan 96 (Deposition) - 11 Jul 96 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Anti-Nitrophenol, Lambda Light Chain, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Yuhasz, C. Parry, M. Strand, L. M. Amzel
Structural Analysis Of Affinity Maturation: The Three-Dimensional Structures Of Complexes Of An Anti-Nitrophenol Antibody.
Mol. Immunol. V. 32 1143 1995
PubMed-ID: 8544863 | Reference-DOI: 10.1016/0161-5890(95)00063-1
(for further references see the PDB file header)

Molecule 1 - 88C6/12 FAB (LIGHT CHAIN)
	Chains	:	L, A
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - 88C6/12 FAB (HEAVY CHAIN)
	Chains	:	H, B
	Engineered	:	YES
	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	NP	2	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NP	-1	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NP	-1	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS H:35 , ARG H:50 , LYS H:59 , TYR H:99 , ALA H:100 , CYS H:102 , HOH H:994 , TRP L:93 , TRP L:98	BINDING SITE FOR RESIDUE NP H 995
2	AC2	SOFTWARE	TRP A:93 , LEU B:33 , HIS B:35 , ARG B:50 , LYS B:59 , TYR B:99 , ALA B:100 , CYS B:102 , GLN H:136	BINDING SITE FOR RESIDUE NP B 996

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	A:137	-	A:196
3	B:22	-	B:96
4	B:145	-	B:200
5	H:22	-	H:96
6	H:145	-	H:200
7	L:22	-	L:90
8	L:137	-	L:196

Asymmetric Unit

No.	Residues
1	Tyr L:143	-	Pro L:144
2	Phe H:151	-	Pro H:152

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

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

(no "Exon" information available for 1YUH)

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 d1yuha1 A:2-109 Immunoglobulin light chain lambda variable domain, VL-lambda                                d1yuha2 A:110-212 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains 1yuhA01 A:2-110 Immunoglobulins                                                                              1yuhA02 A:111-209 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeee........hhh..eeeee.......................eeee.....eeeee....hhh..eeeeeeee..eeee....eeeee.......eeee......hhhh.eeeeeeeee........eee.hhh............eee...eee.eeeeeeehhhhh......eeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuh A   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDRLFTGLIGGTNNRGPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTEGMETTQPSKQSNNKYMASSYLTLSARAWERHASYSCQVTHEGHTVEKSLSRA 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1yuhb1 B:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1yuhb2 B:119-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1yuhB01 B:1-118 Immunoglobulins                                                                                       1yuhB02 B:119-213 Immunoglobulins                                                              ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee......eeeeeee...hhh.eeeeeeee....eeeeeeee...............eeeeee....eeeeee........eeeeeeee............eeeee..........................eeeee............hhh.....eee...........eeeee............eee..........eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuh B   1 QVQFQQSGAELVKPGASVKLSCKASGYTFTSYLMHWIKQRPGRGLEWIGRIDPNNVVTKFNEKFKSKATLTVDKPSSTAYMELSSLTSEDSAVYYCARYAYCRPMDYWGQGTTVTVSSAATTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSDLYTLSSSVTVPASTWPSGTVTCNVAHPASSTAVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1yuhh1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1yuhh2 H:119-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1yuhH01 H:1-118 Immunoglobulins                                                                                       1yuhH02 H:119-217 Immunoglobulins                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eee.eeee...hhh.eeeeeeee....eeeeeeee...eeeee.......eee..........eee....hhh.eeeeeeee.............eeee........eeeee.............eeeeeeee.............................eeeeeee............eeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuh H   1 QVQFQQSGAELVKPGASVKLSCKASGYTFTSYLMHWIKQRPGRGLEWIGRIDPNNVVTKFNEKFKSKATLTVDKPSSTAYMELSSLTSEDSAVYYCARYAYCRPMDYWGQGTTVTVSSAATTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSDLYTLSSSVTVPASTWPSGTVTCNVAHPASSTAVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d1yuhl1 L:2-109 Immunoglobulin light chain lambda variable domain, VL-lambda                                d1yuhl2 L:110-212 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains 1yuhL01 L:2-110 Immunoglobulins                                                                              1yuhL02 L:111-210 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeee........hhh..eeeee.hhh.eeeee.............eeeeee..eeeeee....hhh..eeeeeee....eee....eeee..................hhhh.eeeeeeeeeee....eeeeee.........eee...eee...eeeeeeeeeeehhhhh.....eeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yuh L   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDRLFTGLIGGTNNRGPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTEGMETTQPSKQSNNKYMASSYLTLSARAWERHASYSCQVTHEGHTVEKSLSRA 212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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)

House mouse (Mus musculus) (616)

1a	1yuhB01	B:1-118
1b	1yuhH02	H:119-217
1c	1yuhB02	B:119-213
1d	1yuhA01	A:2-110
1e	1yuhL01	L:2-110
1f	1yuhL02	L:111-210
1g	1yuhA02	A:111-209
1h	1yuhH01	H:1-118

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

Asymmetric Unit(hide GO term definitions)

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		Tyr L:143 - Pro L:144	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

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