4PBW - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CHICKEN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA IN COMPLEX WITH TRKC

Authors :   C. H. Coles, N. Mitakidis, P. Zhang, J. Elegheert, W. Lu, A. W. Stoker, T. A. M. Craig, E. Y. Jones, A. R. Aricescu

Date :   14 Apr 14 (Deposition) - 12 Nov 14 (Release) - 19 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: B,E  (1x)
Biol. Unit 2: A,D  (1x)
Biol. Unit 3: C,F  (1x)

Keywords :   Receptor Protein Tyrosine Phosphatase (Rptp), Synapse Cell Signalling Cell Surface Receptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Coles, N. Mitakidis, P. Zhang, J. Elegheert, W. Lu, A. W. Stoker, T. Nakagawa, A. M. Craig, E. Y. Jones, A. R. Aricescu
Structural Basis For Extracellular Cis And Trans Rptp Sigma Signal Competition In Synaptogenesis.
Nat Commun V. 5 5209 2014
PubMed-ID: 25385546 | Reference-DOI: 10.1038/NCOMMS6209

Molecule 1 - NT-3 GROWTH FACTOR RECEPTOR
	Chains	:	B, A, C
	EC Number	:	2.7.10.1
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	NTRK3, TRKC
	Mutation	:	YES
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	IG3 DOMAIN IS NOT VISIBLE IN ELECTRON DENSITY, SUGGESTING THAT THIS DOMAIN HAD EITHER BEEN PROTEOLYTICALLY CLEAVED DURING CRYSTALLISATION OR IS DISORDERED.
	Synonym	:	NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 3,TRKC TYROSINE KINASE,TRK-C

Molecule 2 - PROTEIN-TYROSINE PHOSPHATASE CRYPALPHA1 ISOFORM
	Chains	:	D, E, F
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	CRYPALPHA1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:		B			E
Biological Unit 2 (1x)	:	A			D
Biological Unit 3 (1x)	:			C			F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:75 , ILE B:76 , ASN B:79 , ALA C:34	binding site for Mono-Saccharide NAG B 401 bound to ASN B 79

Asymmetric Unit

No.	Residues
1	A:32	-	A:38
2	A:36	-	A:45
3	A:164	-	A:189
4	A:166	-	A:207
5	A:231	-	A:284
6	B:32	-	B:38
7	B:36	-	B:45
8	B:164	-	B:189
9	B:166	-	B:207
10	B:231	-	B:284
11	C:32	-	C:38
12	C:36	-	C:45
13	C:164	-	C:189
14	C:166	-	C:207
15	C:231	-	C:284
16	D:53	-	D:106
17	D:155	-	D:206
18	E:53	-	E:106
19	E:155	-	E:206
20	F:53	-	F:106
21	F:155	-	F:206

Asymmetric Unit

No.	Residues
1	Ser B:236	-	Pro B:237
2	Ser A:236	-	Pro A:237
3	Ser C:236	-	Pro C:237
4	Trp C:260	-	Thr C:261
5	Thr C:261	-	Asn C:262
6	Asp D:58	-	Pro D:59
7	Gln D:93	-	Pro D:94
8	Thr D:97	-	Pro D:98
9	Asn D:160	-	Pro D:161
10	Ser D:179	-	Asn D:180
11	Asp E:58	-	Pro E:59
12	Gln E:93	-	Pro E:94
13	Thr E:97	-	Pro E:98
14	Asn E:160	-	Pro E:161
15	Ser E:179	-	Asn E:180
16	Asp F:58	-	Pro F:59
17	Gln F:93	-	Pro F:94
18	Thr F:97	-	Pro F:98
19	Asn F:160	-	Pro F:161
20	Ser F:179	-	Asn F:180

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

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

(no "Exon" information available for 4PBW)

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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..............hhhhhhhhh...eeeee.........hhhhh......eeeee...................eee..........hhhh......eee.........hhhhhhhhhhhh..........eee.....eee............eeee...eeee.....eeeeeeee.....eeee.......eeeeeee.....eeeeeeeee.........eeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbw A  30 TGCPANCLCSKTDINCKKPDDGNLFPLLETSIQITDISRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNLQWTNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVY 302
                                    39        49        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   
                                                       58|                                                                                                                                                                                                                                         
                                                        69

Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..............hhhhhhhhh...eeeee.........hhhhh......eeeee...................eee..........hhhh......eee.........hhhhhhhhhhh...........eee.....eee............eeee...eeee.....eeeeeeee.....eeee.......eeeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbw B  31 GCPANCLCSKTDINCKKPDDGNLFPLLETSIQITDISRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNLQWTNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVY 302
                                    40        50       |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
                                                      58|                                                                                                                                                                                                                                         
                                                       69

Chain C from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee............hhhh...eeeee.........hhhhh......eeeee...................eee..........hhhh......eee.........hhhhhhhhhhh...........eee.....eee............eeee...eeee.....eeeeeeee.....eeee.......eeeeeee.....eeeeeeeee.........eeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbw C  31 GCPANCLCSKTDINCKKPDDGNLFPLTDISRNITSIHIENWKNLQTLNAVDMELYTGLQRLTIRNSGLRNIQPRAFAKNPHLRYIDLSGNRLTTLSWQLFQTLRLFDLRLERNPFQCSCDIRWIQLWQEKGEANLQSQQLHCMNLDTAVILLRNMNITQCDLPEISVSHVNLTVREGENAVITCQGSGSPLPDVDWTVADLHSINTHQTNLQWTNVHAIQLTLVNVTSEDNGFLLTCIAENVVGMSQASVLLTVY 302
                                    40        50     || 77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297     
                                                    56|                                                                                                                                                                                                                                    
                                                     74

Chain D from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee...............eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee.............eee.....eee........eeeeeeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbw D  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRV 226
                                    38        48        58       |73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                                                66|                                                                                                                                                          
                                                                 72

Chain E from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee...............eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee.............eee.....eee........eeeeeeeee..eeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pbw E  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVRVR 227
                                    38        48        58       |73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
                                                                66|                                                                                                                                                           
                                                                 72

Chain F from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee...............eeeeee....eeeeee.........eeeeeeeee..eeeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee.............eee.....eee........eeeeeeeee..eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pbw F  29 ESPPVFIKKPVDQIGVSGGVASFVCQATGDPKPRVTWNVNSQRFETIEFDESAGAVLRIQPLRTPRDENIYECVAQNPHGEVTVHAKLTVLREDQLPPGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSTSNGRIKQLRSGGLQIESSEETDQGKYECVASNSAGVRYSSPANLYVR 225
                                    38        48        58       |73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
                                                                66|                                                                                                                                                         
                                                                 72

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 4PBW)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn D:160 - Pro D:161	[ RasMol ]
		Asn E:160 - Pro E:161	[ RasMol ]
		Asn F:160 - Pro F:161	[ RasMol ]
		Asp D:58 - Pro D:59	[ RasMol ]
		Asp E:58 - Pro E:59	[ RasMol ]
		Asp F:58 - Pro F:59	[ RasMol ]
		Gln D:93 - Pro D:94	[ RasMol ]
		Gln E:93 - Pro E:94	[ RasMol ]
		Gln F:93 - Pro F:94	[ RasMol ]
		Ser A:236 - Pro A:237	[ RasMol ]
		Ser B:236 - Pro B:237	[ RasMol ]
		Ser C:236 - Pro C:237	[ RasMol ]
		Ser D:179 - Asn D:180	[ RasMol ]
		Ser E:179 - Asn E:180	[ RasMol ]
		Ser F:179 - Asn F:180	[ RasMol ]
		Thr C:261 - Asn C:262	[ RasMol ]
		Thr D:97 - Pro D:98	[ RasMol ]
		Thr E:97 - Pro E:98	[ RasMol ]
		Thr F:97 - Pro F:98	[ RasMol ]
		Trp C:260 - Thr C:261	[ RasMol ]

Biological Units
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	4pbw
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	2.7.10.1
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	NTRK3_CHICK \| Q91044	:	4pbv
	PTPRS_CHICK \| F1NWE3	:	2yd4 4pbv

2yd4	2YD4 CONTAINS THE TWO N-TERMINAL IG DOMAINS OF CHICKEN RPTPSIGMA UNCOMPLEXED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (21, 21)

Cis Peptide Bonds (20, 20)

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