2V5T - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NCAM2 IG2-3

Authors :   N. Kulahin, K. K. Rasmussen, O. Kristensen, V. Berezin, E. Bock, P. S. Wa M. Gajhede

Date :   10 Jul 07 (Deposition) - 29 Jul 08 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Phosphorylation, Immunoglobulin Domain, Membrane, Glycoprotein, Cell Adhesion, Transmembrane, Neural Cell Adhesion Molecule (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Kulahin, O. Kristensen, K. K. Rasmussen, L. Olsen, P. Rydberg, B. Vestergaard, J. S. Kastrup, V. Berezin, E. Bock, P. S. Walmod, M. Gajhede
Structural Model And Trans-Interaction Of The Entire Ectodomain Of The Olfactory Cell Adhesion Molecule.
Structure V. 19 203 2011
PubMed-ID: 21300289 | Reference-DOI: 10.1016/J.STR.2010.12.014

Molecule 1 - NEURAL CELL ADHESION MOLECULE 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	KM71H
	Expression System Taxid	:	4922
	Fragment	:	IG2-3, RESIDUES 115-301
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NCAM2, N-CAM 2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:211 , SER A:212 , MET A:213 , LYS A:216 , LYS A:292 , HOH A:1204 , HOH A:1205	BINDING SITE FOR RESIDUE SO4 A1282
2	AC2	SOFTWARE	ARG A:118 , ARG A:137 , LYS A:260 , ARG A:269 , ASN A:270 , GOL A:1287	BINDING SITE FOR RESIDUE SO4 A1283
3	AC3	SOFTWARE	ASN A:175 , ASN A:177 , LYS A:178 , SER A:179 , HOH A:1044 , HOH A:1056 , GOL A:1288	BINDING SITE FOR RESIDUE NAG A1284
4	AC4	SOFTWARE	SER A:217 , ASN A:219 , PHE A:299 , HOH A:1207	BINDING SITE FOR RESIDUE NAG A1285
5	AC5	SOFTWARE	ALA A:167 , GLU A:239	BINDING SITE FOR RESIDUE GOL A1286
6	AC6	SOFTWARE	LYS A:260 , GLY A:261 , SER A:262 , HOH A:1163 , HOH A:1209 , SO4 A:1283	BINDING SITE FOR RESIDUE GOL A1287
7	AC7	SOFTWARE	GLY A:129 , ASP A:131 , NAG A:1284	BINDING SITE FOR RESIDUE GOL A1288
8	AC8	SOFTWARE	ARG A:246 , LYS A:249 , LEU A:250 , TYR A:257 , HOH A:1152	BINDING SITE FOR RESIDUE GOL A1289

Asymmetric/Biological Unit

No.	Residues
1	A:136	-	A:186
2	A:232	-	A:281

Asymmetric/Biological Unit

No.	Residues
1	Ser A:122	-	Pro A:123
2	Ser A:141	-	Pro A:142
3	Ser A:237	-	Pro A:238

(no "SAP(SNP)/Variant" information available for 2V5T)

(no "PROSITE Motif" information available for 2V5T)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000400546	1	ENSE00001543472	chr21:22370633-22370936	304	NCAM2_HUMAN	1-19	19	0	-	-
1.6	ENST00000400546	6	ENSE00001017047	chr21:22652898-22652972	75	NCAM2_HUMAN	19-44	26	0	-	-
1.7	ENST00000400546	7	ENSE00001017039	chr21:22656514-22656720	207	NCAM2_HUMAN	44-113	70	1	A:113-113	1
1.8	ENST00000400546	8	ENSE00001017049	chr21:22658589-22658732	144	NCAM2_HUMAN	113-161	49	1	A:113-161 (gaps)	49
1.10b	ENST00000400546	10b	ENSE00001017037	chr21:22664424-22664561	138	NCAM2_HUMAN	161-207	47	1	A:161-207	47
1.11	ENST00000400546	11	ENSE00001017040	chr21:22696703-22696820	118	NCAM2_HUMAN	207-246	40	1	A:207-246	40
1.12	ENST00000400546	12	ENSE00001017034	chr21:22707825-22707985	161	NCAM2_HUMAN	246-300	55	1	A:246-300	55
1.13b	ENST00000400546	13b	ENSE00001017033	chr21:22710709-22710854	146	NCAM2_HUMAN	300-348	49	1	A:300-301	2
1.14b	ENST00000400546	14b	ENSE00001017041	chr21:22746183-22746333	151	NCAM2_HUMAN	349-399	51	0	-	-
1.15	ENST00000400546	15	ENSE00001017045	chr21:22782594-22782781	188	NCAM2_HUMAN	399-461	63	0	-	-
1.16	ENST00000400546	16	ENSE00001017052	chr21:22790793-22790889	97	NCAM2_HUMAN	462-494	33	0	-	-
1.17	ENST00000400546	17	ENSE00001017031	chr21:22804428-22804601	174	NCAM2_HUMAN	494-552	59	0	-	-
1.19	ENST00000400546	19	ENSE00001017043	chr21:22838927-22839046	120	NCAM2_HUMAN	552-592	41	0	-	-
1.20	ENST00000400546	20	ENSE00001017051	chr21:22840983-22841104	122	NCAM2_HUMAN	592-632	41	0	-	-
1.21	ENST00000400546	21	ENSE00001017035	chr21:22849612-22849792	181	NCAM2_HUMAN	633-693	61	0	-	-
1.22	ENST00000400546	22	ENSE00001017048	chr21:22881172-22881376	205	NCAM2_HUMAN	693-761	69	0	-	-
1.23	ENST00000400546	23	ENSE00001017044	chr21:22906858-22906977	120	NCAM2_HUMAN	761-801	41	0	-	-
1.24b	ENST00000400546	24b	ENSE00001543443	chr21:22910167-22915650	5484	NCAM2_HUMAN	801-837	37	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
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Chain A from PDB  Type:PROTEIN  Length:184
 aligned with NCAM2_HUMAN | O15394 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:189
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
          NCAM2_HUMAN   113 QKLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLYHNEEVTTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQAFLQVFVQ 301
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------I-set-2v5tA01 A:211-298                                                                 --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------I-set-2v5tA02 A:211-298                                                                 --- Pfam domains (2)
         Sec.struct. author ...eeee....eeee....eee..eee.....eeeee.-----.......eee.....eee...hhhhheeeeeeeee....eeeeeeeeeeeeeeeeee....eeeee......eeee.........eeeeee..ee......eeee....eeee...hhhhheeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------Exon 1.10b  PDB: A:161-207 UniProt: 161-207    --------------------------------------Exon 1.12  PDB: A:246-300 UniProt: 246-300             - Transcript 1 (1)
           Transcript 1 (2) Exon 1.8  PDB: A:113-161 (gaps) UniProt: 113-161 ---------------------------------------------Exon 1.11  PDB: A:207-246               -----------------------------------------------------1. Transcript 1 (2)
                 2v5t A 113 SMLTFREVVSPQEFKQGEDAEVVCRVSSSPAPAVSWLY-----TTISDNRFAMLANNNLQILNINKSDEGIYRCEGRVEARGEIDFRDIIVIVNVPPAISMPQKSFNATAERGEEMTFSCRASGSPEPAISWFRNGKLIEENEKYILKGSNTELTVRNIINSDGGPYVCRATNKAGEDEKQAFLQVFVQ 301
                                   122       132       142       | -   |   162       172       182       192       202       212       222       232       242       252       262       272       282       292         
                                                               150   156

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 '\|'

(no "SCOP Domain" information available for 2V5T)

(no "CATH Domain" information available for 2V5T)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: I-set (67)

Homo sapiens (Human) (50)

1a	I-set-2v5tA01	A:211-298
1b	I-set-2v5tA02	A:211-298

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NCAM2_HUMAN | O15394)

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:0007158	neuron cell-cell adhesion	The attachment of a neuron to another cell via adhesion molecules.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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
		Ser A:122 - Pro A:123	[ RasMol ]
		Ser A:141 - Pro A:142	[ RasMol ]
		Ser A:237 - Pro A:238	[ RasMol ]

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	2v5t
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	NCAM2_HUMAN \| O15394	:	2doc 2jll 2kbg 2vaj 2wim 2xy1 2xy2 2xyc

2doc	SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OFHUMAN NEURAL CELL ADHESION MOLECULE 2
2jll	CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3II
2vaj	CRYSTAL STRUCTURE OF NCAM2 IG1 (I4122 CELL UNIT)
2wim	CRYSTAL STRUCTURE OF NCAM2 IG1-3
2xy1	CRYSTAL STRUCTURE OF NCAM2 IG3-4
2xy2	CRYSTAL STRUCTURE OF NCAM2 IG1-2
2xyc	CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (6, 6)

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Gene Ontology (6, 6)

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