2GDC - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF VINCULIN VD1 / IPAA560-633 COMPLEX

Authors :   C. Hamiaux, A. Van Eerde, C. Parsot, J. Broos, B. W. Dijkstra

Date :   15 Mar 06 (Deposition) - 08 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.74

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ipaa/Vinculin Complex, Shigella Flexneri, Helical Bundle Conversion, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Hamiaux, A. Van Eerde, C. Parsot, J. Broos, B. W. Dijkstra
Structural Mimicry For Vinculin Activation By Ipaa, A Virulence Factor Of Shigella Flexneri.
Embo Rep. V. 7 794 2006
PubMed-ID: 16826238 | Reference-DOI: 10.1038/SJ.EMBOR.7400753
(for further references see the PDB file header)

Molecule 1 - VINCULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAL-P2
	Expression System Strain	:	ROSETTA2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	VD1 DOMAIN (RESIDUES 0-265)
	Gene	:	VCL, VINC1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	METAVINCULIN

Molecule 2 - INVASIN IPAA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T2
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL FRAGMENT (RESIDUES 560-633)
	Gene	:	IPAA
	Organism Scientific	:	SHIGELLA FLEXNERI
	Organism Taxid	:	623
	Synonym	:	70 KDA ANTIGEN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	UNK	10	Mod. Amino Acid

(no "Site" information available for 2GDC)

(no "SS Bond" information available for 2GDC)

(no "Cis Peptide Bond" information available for 2GDC)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VINCULIN_1	PS00663	Vinculin family talin-binding region signature.	VINC_CHICK	162-182	1	A:162-182

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSGALT00000008145	1	ENSGALE00000053744	chr6:16537808-16537722	87	VINC_CHICK	1-29	29	1	A:2-22	21
1.2	ENSGALT00000008145	2	ENSGALE00000053740	chr6:16519003-16518933	71	VINC_CHICK	30-53	24	1	A:34-53	20
1.3a	ENSGALT00000008145	3a	ENSGALE00000053756	chr6:16512719-16512569	151	VINC_CHICK	53-103	51	1	A:53-103	51
1.4	ENSGALT00000008145	4	ENSGALE00000053745	chr6:16510654-16510546	109	VINC_CHICK	104-140	37	1	A:104-140	37
1.5	ENSGALT00000008145	5	ENSGALE00000053754	chr6:16508878-16508756	123	VINC_CHICK	140-181	42	1	A:140-181	42
1.6	ENSGALT00000008145	6	ENSGALE00000053758	chr6:16507252-16507092	161	VINC_CHICK	181-234	54	1	A:181-234	54
1.7	ENSGALT00000008145	7	ENSGALE00000053751	chr6:16501242-16501152	91	VINC_CHICK	235-265	31	1	A:235-250	16
1.8	ENSGALT00000008145	8	ENSGALE00000053757	chr6:16499876-16499729	148	VINC_CHICK	265-314	50	0	-	-
1.9	ENSGALT00000008145	9	ENSGALE00000053755	chr6:16499239-16499086	154	VINC_CHICK	314-365	52	0	-	-
1.10	ENSGALT00000008145	10	ENSGALE00000053750	chr6:16498296-16498121	176	VINC_CHICK	366-424	59	0	-	-
1.11b	ENSGALT00000008145	11b	ENSGALE00000267361	chr6:16496998-16496808	191	VINC_CHICK	424-488	65	0	-	-
1.12	ENSGALT00000008145	12	ENSGALE00000053753	chr6:16496312-16496113	200	VINC_CHICK	488-554	67	0	-	-
1.13b	ENSGALT00000008145	13b	ENSGALE00000267355	chr6:16495519-16495387	133	VINC_CHICK	555-599	45	0	-	-
1.14	ENSGALT00000008145	14	ENSGALE00000267347	chr6:16494529-16494528	2	VINC_CHICK	599-599	1	0	-	-
1.15	ENSGALT00000008145	15	ENSGALE00000053736	chr6:16494431-16494282	150	VINC_CHICK	600-649	50	0	-	-
1.16	ENSGALT00000008145	16	ENSGALE00000053752	chr6:16493681-16493573	109	VINC_CHICK	650-686	37	0	-	-
1.17	ENSGALT00000008145	17	ENSGALE00000053743	chr6:16492582-16492280	303	VINC_CHICK	686-787	102	0	-	-
1.18	ENSGALT00000008145	18	ENSGALE00000053738	chr6:16491676-16491552	125	VINC_CHICK	787-828	42	0	-	-
1.19	ENSGALT00000008145	19	ENSGALE00000053737	chr6:16491215-16491030	186	VINC_CHICK	829-890	62	0	-	-
1.20	ENSGALT00000008145	20	ENSGALE00000053759	chr6:16488005-16487799	207	VINC_CHICK	891-959	69	0	-	-
1.21	ENSGALT00000008145	21	ENSGALE00000053749	chr6:16485617-16485414	204	VINC_CHICK	960-1027	68	0	-	-
1.22	ENSGALT00000008145	22	ENSGALE00000053741	chr6:16484789-16484685	105	VINC_CHICK	1028-1062	35	0	-	-
1.23b	ENSGALT00000008145	23b	ENSGALE00000267322	chr6:16484014-16483843	172	VINC_CHICK	1063-1110	48	0	-	-

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:238
 aligned with VINC_CHICK | P12003 from UniProtKB/Swiss-Prot  Length:1135

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           VINC_CHICK     2 PVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAEINEIIRVLQL 250
               SCOP domains d2gdca1 A:2-128 autom           ated matches                                                                                   d2gdca2 A:129-250 automated matches                                                                                        SCOP domains
               CATH domains 2gdcA01 A:2-129 vbs2            fragment of talin                                                                               2gdcA02 A:130-250  [code=1.20.120.230, no name defined]                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh..-----------......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------VINCULIN_1           -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-22       Exon 1.2  PDB: A:34-53  --------------------------------------------------Exon 1.4  PDB: A:104-140             ----------------------------------------Exon 1.6  PDB: A:181-234 UniProt: 181-234             Exon 1.7         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3a  PDB: A:53-103 UniProt: 53-103           ------------------------------------Exon 1.5  PDB: A:140-181 UniProt: 140-181 --------------------------------------------------------------------- Transcript 1 (2)
                 2gdc A   2 PVFHTRTIESILEPVAQQISH-----------GKAIPDLTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAEINEIIRVLQL 250
                                    11        21|        -  |     41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                               22          34

Chain B from PDB  Type:PROTEIN  Length:21
 aligned with IPAA_SHIFL | P18010 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:21
                                   619       629 
           IPAA_SHIFL   610 NNIYKAAKDVTTSLSKVLKNI 630
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 2gdc B 610 xxIYxxAKxVxxxLSKVLxxI 630
                            ||  || 619|||    629 
                            ||  ||  | |||    629-UNK
                          610-UNK|  | |||     |  
                           611-UNK  | |||     |  
                              614-UNK |||     |  
                               615-UNK|||     |  
                                  618-UNK     |  
                                    620-UNK   |  
                                     621-UNK  |  
                                      622-UNK |

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: alpha-catenin/vinculin-like (25)

Family: alpha-catenin/vinculin (24)

Protein domain: automated matches (8)

Chicken (Gallus gallus) [TaxId: 9031] (3)

1a	d2gdca1	A:2-128
1b	d2gdca2	A:129-250

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.230, no name defined] (23)

Chicken (Gallus gallus) (9)

2gdcA02

A:130-250

Topology: vbs2 fragment of talin (15)

Homologous Superfamily: vbs2 fragment of talin (15)

Chicken (Gallus gallus) (7)

2gdcA01

A:2-129

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VINC_CHICK | P12003)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0051393	alpha-actinin binding	Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats.
	GO:0045294	alpha-catenin binding	Interacting selectively and non-covalently with the alpha subunit of the catenin complex.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0045296	cadherin binding	Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
	GO:0002162	dystroglycan binding	Interacting selectively and non-covalently with dystroglycan. Dystroglycan is glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-covalently associated subunits, alpha (N-terminal) and beta (C-terminal).
	GO:0051371	muscle alpha-actinin binding	Interacting selectively and non-covalently with muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0097110	scaffold protein binding	Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0017166	vinculin binding	Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane.
biological process
	GO:0034333	adherens junction assembly	The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
	GO:0043297	apical junction assembly	The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents.
	GO:0048675	axon extension	Long distance growth of a single axon process involved in cellular development.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0090136	epithelial cell-cell adhesion	The attachment of an epithelial cell to another epithelial cell via adhesion molecules.
	GO:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0002009	morphogenesis of an epithelium	The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
	GO:0070527	platelet aggregation	The adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0034394	protein localization to cell surface	A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
cellular component
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005913	cell-cell adherens junction	An adherens junction which connects a cell to another cell.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0043034	costamere	Regular periodic sub membranous arrays of vinculin in skeletal and cardiac muscle cells, these arrays link Z-discs to the sarcolemma and are associated with links to extracellular matrix.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	GO:0005916	fascia adherens	A cell-cell adherens junction that contains the transmembrane protein N-cadherin, which interacts with identical molecules from neighboring cells to form a tight mechanical intercellular link; forms a large portion of the intercalated disc, the structure at which myofibrils terminate in cardiomyocytes.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0090637	inner dense plaque of desmosome	The desmosomal part containing the C-termini of desmoplakins which interact with the keratin intermediate filaments, serving to tether the intermediate filaments to the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005927	muscle tendon junction	A cell-substrate junction found at the terminal anchorage site of skeletal muscle cells to tendons.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0090636	outer dense plaque of desmosome	The desmosomal part containing plakoglobins, plakophilins, the N-termini of desmoplakins, as well as the cytoplasmic tails of the desmosomal cadherins, which together attach the plaque to the plasma membrane.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0042383	sarcolemma	The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
	GO:0098723	skeletal muscle myofibril	A myofibril of a skeletal muscle fiber.
	GO:0030486	smooth muscle dense body	Electron-dense region associated with a smooth muscle contractile fiber.
	GO:0001725	stress fiber	A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.
	GO:1990357	terminal web	An actin-rich cytoskeletal network located beneath the microvilli of the apical plasma membrane of polarized epithelial cells. In addition to actin filaments, the terminal web may contain actin-binding proteins, myosin motor proteins, and intermediate filaments. The terminal web can function as a contractile structure that influences the spatial distribution of microvilli as well as the development and morphogenesis of tissues containing polarized epithelial cells.
	GO:0005915	zonula adherens	A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.

Chain B (IPAA_SHIFL | P18010)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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:0017166	vinculin binding	Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane.
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.
	GO:0030836	positive regulation of actin filament depolymerization	Any process that activates or increases the frequency, rate or extent of actin depolymerization.
cellular component
	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.

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
		UNK	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gdc)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2gdc
		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
	IPAA_SHIFL \| P18010
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	VINC_CHICK \| P12003
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	IPAA_SHIFL \| P18010
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	VINC_CHICK \| P12003
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2GDC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (7, 7)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (57, 60)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File