1L3W - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   C-CADHERIN ECTODOMAIN

Authors :   T. J. Boggon, J. Murray, S. Chappuis-Flament, E. Wong, B. M. Gumbiner, L

Date :   01 Mar 02 (Deposition) - 26 Apr 02 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.08

Chains :   Asym./Biol. Unit : A

Keywords :   Cell Adhesion, Calcium Binding, Cadherin, Extracellular, Ectodomain, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. J. Boggon, J. Murray, S. Chappuis-Flament, E. Wong, B. M. Gumbiner, L. Shapiro
C-Cadherin Ectodomain Structure And Implications For Cell Adhesion Mechanisms
Science V. 296 1308 2002
PubMed-ID: 11964443 | Reference-DOI: 10.1126/SCIENCE.1071559

Molecule 1 - EP-CADHERIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell	:	CHOKI CELLS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Expression System Tissue	:	SECRETION
	Expression System Vector	:	PEE14
	Fragment	:	C-CADHERIN ECTODOMAIN
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	C-CADHERIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 27)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	NAG	11	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	4	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:154 , PRO A:155 , GLU A:186 , TYR A:187 , THR A:188	BINDING SITE FOR RESIDUE NAG A 801
02	AC2	SOFTWARE	ASP A:222 , THR A:245	BINDING SITE FOR RESIDUE NAG A 802
03	AC3	SOFTWARE	VAL A:258 , TYR A:259 , ILE A:271 , THR A:272 , THR A:273	BINDING SITE FOR RESIDUE NAG A 803
04	AC4	SOFTWARE	PHE A:308 , LEU A:312 , THR A:314	BINDING SITE FOR RESIDUE NDG A 804
05	AC5	SOFTWARE	THR A:301 , THR A:314 , THR A:316 , NAG A:806	BINDING SITE FOR RESIDUE NAG A 805
06	AC6	SOFTWARE	THR A:225 , GLN A:299 , THR A:316 , THR A:318 , NAG A:805	BINDING SITE FOR RESIDUE NAG A 806
07	AC7	SOFTWARE	THR A:227 , VAL A:297 , THR A:320	BINDING SITE FOR RESIDUE NAG A 807
08	AC8	SOFTWARE	TYR A:406 , THR A:407	BINDING SITE FOR RESIDUE NAG A 808
09	AC9	SOFTWARE	LEU A:411 , VAL A:419 , GLY A:420 , THR A:421 , NAG A:810	BINDING SITE FOR RESIDUE NAG A 809
10	BC1	SOFTWARE	THR A:421 , THR A:423 , NAG A:809 , NDG A:811	BINDING SITE FOR RESIDUE NAG A 810
11	BC2	SOFTWARE	ALA A:335 , ILE A:409 , THR A:425 , NAG A:810	BINDING SITE FOR RESIDUE NDG A 811
12	BC3	SOFTWARE	TYR A:226 , THR A:227 , ALA A:228 , GLN A:240	BINDING SITE FOR RESIDUE NAG A 812
13	BC4	SOFTWARE	ASN A:403	BINDING SITE FOR RESIDUE NDG A 902
14	BC5	SOFTWARE	ASN A:270	BINDING SITE FOR RESIDUE NDG A 903
15	BC6	SOFTWARE	VAL A:524 , ASN A:526	BINDING SITE FOR RESIDUE NAG A 904
16	BC7	SOFTWARE	ASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:143 , ASP A:195	BINDING SITE FOR RESIDUE CA A 600
17	BC8	SOFTWARE	GLU A:11 , GLU A:69 , ASP A:100 , GLN A:101 , ASP A:103 , ASP A:136	BINDING SITE FOR RESIDUE CA A 601
18	BC9	SOFTWARE	GLU A:11 , ASN A:12 , ASP A:67 , GLU A:69 , ASP A:103	BINDING SITE FOR RESIDUE CA A 602
19	CC1	SOFTWARE	GLU A:119 , GLU A:182 , ASP A:213 , ALA A:214 , ASP A:216 , ASP A:248	BINDING SITE FOR RESIDUE CA A 603
20	CC2	SOFTWARE	GLU A:119 , ASP A:180 , GLU A:182 , ASP A:216	BINDING SITE FOR RESIDUE CA A 604
21	CC3	SOFTWARE	ASN A:215 , ASN A:217 , ASP A:246 , ASP A:248 , ALA A:254 , ASN A:304	BINDING SITE FOR RESIDUE CA A 605
22	CC4	SOFTWARE	GLU A:232 , ASP A:289 , GLU A:291 , GLU A:328 , CA A:610	BINDING SITE FOR RESIDUE CA A 606
23	CC5	SOFTWARE	ASN A:327 , GLU A:328 , ASP A:358 , ASP A:360 , GLN A:365 , ASP A:414	BINDING SITE FOR RESIDUE CA A 607
24	CC6	SOFTWARE	GLU A:343 , ASP A:395 , GLU A:397 , ASP A:435 , CA A:611	BINDING SITE FOR RESIDUE CA A 608
25	CC7	SOFTWARE	ASN A:434 , ASN A:436 , ASP A:461 , ASP A:463 , ASN A:467 , ASP A:515	BINDING SITE FOR RESIDUE CA A 609
26	CC8	SOFTWARE	GLU A:232 , GLU A:291 , ASP A:325 , VAL A:326 , GLU A:328 , ASP A:360 , CA A:606	BINDING SITE FOR RESIDUE CA A 610
27	CC9	SOFTWARE	GLU A:343 , GLU A:397 , ASP A:432 , VAL A:433 , ASP A:435 , ASP A:463 , CA A:608	BINDING SITE FOR RESIDUE CA A 611

Asymmetric/Biological Unit

No.	Residues
1	A:448	-	A:532
2	A:530	-	A:539

Asymmetric/Biological Unit

No.	Residues
1	Phe A:17	-	Pro A:18
2	Pro A:46	-	Pro A:47
3	Glu A:157	-	Pro A:158
4	Pro A:465	-	Pro A:466

(no "SAP(SNP)/Variant" information available for 1L3W)

Asymmetric/Biological Unit (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CADHERIN_2	PS50268	Cadherins domain profile.	CADHF_XENLA	156-263 264-376 377-487 488-599	4	A:1-108 A:109-221 A:222-332 A:333-444
2	CADHERIN_1	PS00232	Cadherin domain signature.	CADHF_XENLA	251-261 364-374 583-593	3	A:96-106 A:209-219 A:428-438

(no "Exon" information available for 1L3W)

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:540
 aligned with CADHF_XENLA | P33148 from UniProtKB/Swiss-Prot  Length:880

    Alignment length:540
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695
          CADHF_XENLA   156 DWVIPPIKVSENERGPFPKRLVQIKSNKDRFNKVYYSITGQGADNPPQGVFRIEWETGWMLVTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVIDQNDNRPKFTQDVFRGSVREGVQPGTQVMAVSATDEDDNIDSLNGVLSYSILKQDPEEPIPNLFTINRETGVISLIGTGLDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFEVQRLSVTDLDMPGTPAWQAVYKIRVNEGGFFNITTDPESNQGILTTAKGLDFELRKQYVLQITVENAEPFSVPLPTSTATVTVTVEDVNEAPFFVPAVSRVDVSEDLSRGEKIISLVAQDPDKQQIQKLSYFIGNDPARWLTVNKDNGIVTGNGNLDRESEYVKNNTYTVIMLVTDDGVSVGTGTGTLILHVLDVNDNGPVPSPRVFTMCDQNPEPQVLTISDADIPPNTYPYKVSLSHGSDLTWKAELDSKGTSMLLSPTQQLKKGDYSIYVLLSDAQNNPQLTVVNATVCSCEGKAIKCQ 695
               SCOP domains d1l3wa1 A:1-100 C-cadherin ectodomain                                                               d1l3wa2 A:101-213 C-cadherin ectodomain                                                                          d1l3wa3 A:214-326 C-cadherin ectodomain                                                                          d1l3wa4 A:327-433 C-cadherin ectodomain                                                                    d1l3wa5 A:434-540 C-cadherin ectodomain                                                                     SCOP domains
               CATH domains 1l3wA01 A:1-101 Cadherins                                                                            1l3wA02 A:102-213 Cadherins                                                                                     1l3wA03 A:214-327 Cadherins                                                                                       1l3wA04 A:328-433 Cadherins                                                                               1l3wA05 A:434-540 Cadherins                                                                                 CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cadherin-1l3wA01 A:443-530                                                              ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cadherin-1l3wA02 A:443-530                                                              ---------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cadherin-1l3wA03 A:443-530                                                              ---------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cadherin-1l3wA04 A:443-530                                                              ---------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cadherin-1l3wA05 A:443-530                                                              ---------- Pfam domains (5)
         Sec.struct. author ..................eeeee...hhhhh..eeeeeee..................eeee..........eeeeeeeeee.........eeeeeeee................................................eeeeee.........eee.....eeee...........eeeeeeeeehhhhh..eee..eeeeee........................................................eeeee......eeeee...........eeeee................eeeeeeee.......................................................eee....eeee................eeeeeeee.........eeee.................................................................eeee........................eeee..eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) CADHERIN_2  PDB: A:1-108 UniProt: 156-263                                                                   CADHERIN_2  PDB: A:109-221 UniProt: 264-376                                                                      CADHERIN_2  PDB: A:222-332 UniProt: 377-487                                                                    CADHERIN_2  PDB: A:333-444 UniProt: 488-599                                                                     ------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------------CADHERIN_1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l3w A   1 DWVIPPIKVSENERGPFPKRLVQIKSNKDRFNKVYYSITGQGADNPPQGVFRIEWETGWMLVTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVIDQNDNRPKFTQDVFRGSVREGVQPGTQVMAVSATDEDDNIDSLNGVLSYSILKQDPEEPIPNLFTINRETGVISLIGTGLDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFEVQRLSVTDLDMPGTPAWQAVYKIRVNEGGFFNITTDPESNQGILTTAKGLDFELRKQYVLQITVENAEPFSVPLPTSTATVTVTVEDVNEAPFFVPAVSRVDVSEDLSRGEKIISLVAQDPDKQQIQKLSYFIGNDPARWLTVNKDNGIVTGNGNLDRESEYVKNNTYTVIMLVTDDGVSVGTGTGTLILHVLDVNDNGPVPSPRVFTMCDQNPEPQVLTISDADIPPNTYPYKVSLSHGSDLTWKAELDSKGTSMLLSPTQQLKKGDYSIYVLLSDAQNNPQLTVVNATVCSCEGKAIKCQ 540
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540

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 beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Cadherin-like (44)

Family: Cadherin (30)

Protein domain: C-cadherin ectodomain (1)

African clawed frog (Xenopus laevis) [TaxId: 8355] (1)

1a	d1l3wa1	A:1-100
1b	d1l3wa2	A:101-213
1c	d1l3wa3	A:214-326
1d	d1l3wa4	A:327-433
1e	d1l3wa5	A:434-540

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cadherins (28)

African clawed frog (Xenopus laevis) (1)

1a	1l3wA01	A:1-101
1b	1l3wA02	A:102-213
1c	1l3wA04	A:328-433
1d	1l3wA05	A:434-540
1e	1l3wA03	A:214-327

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: Cadherin (41)

Xenopus laevis (African clawed frog) (2)

1a	Cadherin-1l3wA01	A:443-530
1b	Cadherin-1l3wA02	A:443-530
1c	Cadherin-1l3wA03	A:443-530
1d	Cadherin-1l3wA04	A:443-530
1e	Cadherin-1l3wA05	A:443-530

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CADHF_XENLA | P33148)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:157 - Pro A:158	[ RasMol ]
		Phe A:17 - Pro A:18	[ RasMol ]
		Pro A:46 - Pro A:47	[ RasMol ]
		Pro A:465 - Pro A:466	[ RasMol ]

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	1l3w
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1edh	E-CADHERIN 2-DOMAIN CRYSTAL STRUCTURE
1ff5	E-CADHERIN 2-DOMAIN CRYSTAL STRUCTURE
1ncg	N-CADHERIN 1-DOMAIN CRYSTAL STRUCTURE
1nch	N-CADHERIN 1-DOMAIN CRYSTAL STRUCTURE
1nci	N-CADHERIN 1-DOMAIN CRYSTAL STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 27)

Sites (27, 27)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 7)

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