2VMC - JenaLib

Title :   STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM WITH N-ACETYL-GALACTOSAMINE

Authors :   K. Saboia, M. Satre, A. Imberty, A. Varrot

Date :   25 Jan 08 (Deposition) - 01 Jul 08 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Ddr, Lectin, Aggregation, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Aragao, M. Satre, A. Imberty, A. Varrot
Structure Determination Of Discoidin Ii From Dictyostelium Discoideum And Carbohydrate Binding Properties Of The Lectin Domain.
Proteins V. 73 43 2008
PubMed-ID: 18384150 | Reference-DOI: 10.1002/PROT.22038

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:212	BINDING SITE FOR RESIDUE CL A 498
2	AC2	SOFTWARE	TRP A:219	BINDING SITE FOR RESIDUE CL A 499
3	AC3	SOFTWARE	ASN A:39 , SER A:40 , ASP A:47 , HOH A:2078 , HOH A:2082 , HOH A:2098 , HOH A:2099	BINDING SITE FOR RESIDUE CA A 500
4	AC4	SOFTWARE	ASP A:209 , GLN A:216 , ARG A:218 , TRP A:238 , TYR A:244 , NGA A:505 , HOH A:2336 , HOH A:2352 , HOH A:2353 , HOH A:2354 , HOH A:2355 , HOH A:2356	BINDING SITE FOR RESIDUE A2G A 501
5	AC5	SOFTWARE	ASP A:209 , GLN A:216 , ARG A:218 , TRP A:238 , TYR A:244 , A2G A:501 , HOH A:2336 , HOH A:2352 , HOH A:2354 , HOH A:2355 , HOH A:2356	BINDING SITE FOR RESIDUE NGA A 505
6	AC6	SOFTWARE	SER A:9 , ALA A:12 , ARG A:94 , TRP A:102 , ALA A:135 , HIS A:137 , HOH A:2162	BINDING SITE FOR RESIDUE 1PG A 502
7	AC7	SOFTWARE	TYR A:24 , HIS A:28 , SER A:53 , ARG A:81 , HIS A:84 , GLN A:86 , HOH A:2057 , HOH A:2358	BINDING SITE FOR RESIDUE 1PG A 503
8	AC8	SOFTWARE	SER A:7	BINDING SITE FOR RESIDUE EDO A 504

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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:252
 aligned with DIS2_DICDI | P42530 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:252
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
           DIS2_DICDI     6 GSVSCLANALLNLRSSTDYNADHGVKNSILNFSNSKDASRFDGSESWSSSVLDKNQFIVAGSDSVKHFVAISTQGRGDHDQWVTSYKLRYTLDNVNWVEYNNGEIINANKDRNSIVTINFNPPIKARSIAIHPQTYNNHISLRWELYALPVKSYSNPSVQVGEVSIGDRSLNSGTGSRTIVRHVKFPVEFLSVPIVSIGCKKVDAHTDNGQMRWEGKSENITTKGFDLTFITWGNNAVYDLTFDYVAVEFNN 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------F5_F8_type_C-2vmcA01 A:17-151                                                                                                          -------------------------------H_lectin-2vmcA02 A:183-255                                               -- Pfam domains
         Sec.struct. author ....hhhhh..eeee..........................................eeee....eeeeeeeee.......eeeeeeeeee.....eee......eeee......eeeee...eeeeeeeeeeeeee...eeeeeeee.........eeeeeeee............eeeeeeee.........eeeeeeeeeee.........eeeee.....eeeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----FA58C_3  PDB: A:10-154 UniProt: 10-154                                                                                                           ------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------FA58C_1  PDB: A:51-80         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vmc A   6 GSVSCLANALLNLRSSTDYNADHGVKNSILNFSNSKDASRFDGSESWSSSVLDKNQFIVAGSDSVKHFVAISTQGRGDHDQWVTSYKLRYTLDNVNWVEYNNGEIINANKDRNSIVTINFNPPIKARSIAIHPQTYNNHISLRWELYALPVKSYSNPSVQVGEVSIGDRSLNSGTGSRTIVRHVKFPVEFLSVPIVSIGCKKVDAHTDNGQMRWEGKSENITTKGFDLTFITWGNNAVYDLTFDYVAVEFNN 257
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

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 (0, 0)

Pfam Domains (2, 2)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (DIS2_DICDI | P42530)

molecular function
	GO:0046871	N-acetylgalactosamine binding	Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016936	galactoside binding	Interacting selectively and non-covalently with any glycoside in which the sugar group is galactose.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0070492	oligosaccharide binding	Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
	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:0098609	cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules.
	GO:0044351	macropinocytosis	An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
	GO:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
	GO:0046689	response to mercury ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
cellular component
	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:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

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