4PLM - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3)

Authors :   K. Xu, D. B. Nikolov

Date :   18 May 14 (Deposition) - 18 Jun 14 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Elongated, Cysteine Rich, Glycoprotein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Xu, Z. Wu, N. Renier, A. Antipenko, D. Tzvetkova-Robev, Y. Xu, M. Minchenko, V. Nardi-Dei, K. R. Rajashankar, J. Himanen, M. Tessier-Lavigne, D. B. Nikolov
Neural Migration. Structures Of Netrin-1 Bound To Two Receptors Provide Insight Into Its Axon Guidance Mechanism.
Science V. 344 1275 2014
PubMed-ID: 24876346 | Reference-DOI: 10.1126/SCIENCE.1255149

Molecule 1 - NETRIN-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	BACULOVIRIDAE
	Expression System Taxid	:	10442
	Fragment	:	LN-LE3 (UNP RESIDUES 26-457)
	Gene	:	NTN1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:109 , ASP A:112 , THR A:120 , SER A:279 , HOH A:656	binding site for residue CA A 504
2	AC2	SOFTWARE	ARG A:157 , LEU A:393	binding site for residue CL A 505
3	AC3	SOFTWARE	HIS A:105 , CYS A:121 , MG A:507	binding site for residue CL A 506
4	AC4	SOFTWARE	GLN A:123 , CL A:506	binding site for residue MG A 507
5	AC5	SOFTWARE	ASN A:97 , SER A:99 , HOH A:679	binding site for Mono-Saccharide NAG A 501 bound to ASN A 97
6	AC6	SOFTWARE	ASN A:118	binding site for Mono-Saccharide NAG A 502 bound to ASN A 118
7	AC7	SOFTWARE	ASN A:133	binding site for Mono-Saccharide NAG A 503 bound to ASN A 133

Asymmetric Unit

No.	Residues
1	A:43	-	A:53
2	A:72	-	A:96
3	A:80	-	A:93
4	A:121	-	A:154
5	A:183	-	A:205
6	A:287	-	A:296
7	A:289	-	A:306
8	A:308	-	A:317
9	A:320	-	A:340
10	A:343	-	A:352
11	A:345	-	A:370
12	A:373	-	A:382
13	A:385	-	A:403
14	A:406	-	A:418
15	A:408	-	A:425
16	A:427	-	A:436
17	A:439	-	A:453

Asymmetric Unit

No.	Residues
1	Lys A:74	-	Pro A:75
2	Tyr A:130	-	Pro A:131
3	Val A:212	-	Arg A:213
4	Arg A:213	-	Pro A:214
5	Gly A:260	-	Asp A:261

(no "SAP(SNP)/Variant" information available for 4PLM)

(no "PROSITE Motif" information available for 4PLM)

(no "Exon" information available for 4PLM)

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
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Chain A from PDB  Type:PROTEIN  Length:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee.......ee........eeeeeeeee..eeeeeeeee...hhhhh.hhhhh...........ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee.hhhhhhh................ee...........eeeeee......hhhhhhhhhhhhhhheeeeeeeee.....................eeeeeeeeeee........eee.....eee.....ee.....ee..............................eeeehhhhhhhh.....eeee.....ee.....ee...eee...........eee.........................ee.....ee...eee.......eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plm A  40 PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDEDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIP 457
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 ||    271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
                                                                                                                                                                                                                                                       261|                                                                                                                                                                                                 
                                                                                                                                                                                                                                                        264

Legend:		→ Mismatch	(orange background)
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	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 4PLM)

(no "CATH Domain" information available for 4PLM)

(no "Pfam Domain" information available for 4PLM)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Arg A:213 - Pro A:214	[ RasMol ]
		Gly A:260 - Asp A:261	[ RasMol ]
		Lys A:74 - Pro A:75	[ RasMol ]
		Tyr A:130 - Pro A:131	[ RasMol ]
		Val A:212 - Arg A:213	[ RasMol ]

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	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4plm
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	NET1_CHICK \| Q90922
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	NET1_CHICK \| Q90922	:	4pln 4plo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (17, 17)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (21, 21)

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