3DO3 - JenaLib

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	NAG A:2 , FUL A:8 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , THR A:299	BINDING SITE FOR RESIDUE NAG A 1
02	AC2	SOFTWARE	NAG A:1 , BMA A:3 , MAN A:4 , ARG A:301	BINDING SITE FOR RESIDUE NAG A 2
03	AC3	SOFTWARE	NAG A:2 , MAN A:4 , MAN A:6 , PHE A:243	BINDING SITE FOR RESIDUE BMA A 3
04	AC4	SOFTWARE	NAG A:2 , BMA A:3 , NAG A:5 , PHE A:243 , ARG A:301	BINDING SITE FOR RESIDUE MAN A 4
05	AC5	SOFTWARE	MAN A:4 , GAL A:7 , PHE A:243 , THR A:260 , HOH A:499	BINDING SITE FOR RESIDUE NAG A 5
06	AC6	SOFTWARE	BMA A:3 , NAG A:9 , BMA B:3 , MAN B:6	BINDING SITE FOR RESIDUE MAN A 6
07	AC7	SOFTWARE	NAG A:5 , PRO A:244 , LYS A:246 , ASP A:249 , GLU A:258 , THR A:260 , ASN B:384	BINDING SITE FOR RESIDUE GAL A 7
08	AC8	SOFTWARE	NAG A:1 , GLU A:272	BINDING SITE FOR RESIDUE FUL A 8
09	AC9	SOFTWARE	MAN A:6	BINDING SITE FOR RESIDUE NAG A 9
10	BC1	SOFTWARE	NAG B:2 , FUL B:8 , VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , THR B:299	BINDING SITE FOR RESIDUE NAG B 1
11	BC2	SOFTWARE	NAG B:1 , BMA B:3 , FUL B:8 , PHE B:241 , VAL B:264	BINDING SITE FOR RESIDUE NAG B 2
12	BC3	SOFTWARE	MAN A:6 , NAG B:2 , MAN B:4 , MAN B:6 , PHE B:241 , PHE B:243	BINDING SITE FOR RESIDUE BMA B 3
13	BC4	SOFTWARE	BMA B:3 , NAG B:5 , PHE B:243	BINDING SITE FOR RESIDUE MAN B 4
14	BC5	SOFTWARE	MAN B:4 , GAL B:7 , PHE B:243 , THR B:260	BINDING SITE FOR RESIDUE NAG B 5
15	BC6	SOFTWARE	MAN A:6 , BMA B:3 , NAG B:9	BINDING SITE FOR RESIDUE MAN B 6
16	BC7	SOFTWARE	ASN A:384 , NAG B:5 , PRO B:244 , LYS B:246 , GLU B:258 , THR B:260	BINDING SITE FOR RESIDUE GAL B 7
17	BC8	SOFTWARE	NAG B:1 , NAG B:2	BINDING SITE FOR RESIDUE FUL B 8
18	BC9	SOFTWARE	MAN B:6 , LYS B:334	BINDING SITE FOR RESIDUE NAG B 9

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (1, 2)

Exons (2, 4)

Sequences/Alignments

Asymmetric/Biological 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:209
 aligned with IGHG1_HUMAN | P01857 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:209
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         
          IGHG1_HUMAN   119 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 327
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --3do3A01 A:238-337 Immunoglobulins                                                                   3do3A02 A:338-443 Immunoglobulins                                                                         - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhh.....eeeeeeeee......eeeeeee..eee...ee..........eeeeeeee.hhhhhhh...eeeeeee......eeeee..........eeeee..hhhhh....eeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeehhhhhh...eeeeeee...hhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------E-M-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:236-341 UniProt: 114-224 [INCOMPLETE]                                                   ------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.4c  PDB: A:341-444 UniProt: 224-330 [INCOMPLETE]                                                  Transcript 1 (2)
                 3do3 A 236 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS 444
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with IGHG1_HUMAN | P01857 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:210
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328
          IGHG1_HUMAN   119 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP 328
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --3do3B01 B:238-337 Immunoglobulins                                                                   3do3B02 B:338-443 Immunoglobulins                                                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhh.....eee...............eeee.........................eee.hhhhhhh...eeee............ee..........eeeee..hhhhh...eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh..eeeeeee...hhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------E-M--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:236-341 UniProt: 114-224 [INCOMPLETE]                                                   -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------Exon 1.4c  PDB: B:341-445 UniProt: 224-330 [INCOMPLETE]                                                   Transcript 1 (2)
                 3do3 B 236 GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP 445
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IGHG1_HUMAN | P01857)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:373 - Pro A:374	[ RasMol ]
		Tyr B:373 - Pro B:374	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3do3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IGHG1_HUMAN \| P01857
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 18)

Sites (18, 18)