5DN2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   HUMAN NRP2 B1 DOMAIN IN COMPLEX WITH THE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF VEGF-A

Authors :   Y. C. I. Tsai, P. Frankel, C. Fotinou, R. Rana, I. Zachary, S. Djordjevic

Date :   09 Sep 15 (Deposition) - 20 Jul 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,G  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C,E  (1x)
Biol. Unit 4: D,F  (1x)

Keywords :   Signaling Protein, Neuropilin-2, Vegfa, Angiogenesis, Heparin, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. C. Tsai, C. Fotinou, R. Rana, T. Yelland, P. Frankel, I. Zachary, S. Djordjevic
Structural Studies Of Neuropilin-2 Reveal A Zinc Ion Bindin Site Remote From The Vascular Endothelial Growth Factor Binding Pocket.
Febs J. V. 283 1921 2016
PubMed-ID: 26991001 | Reference-DOI: 10.1111/FEBS.13711

Molecule 1 - NEUROPILIN-2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B-TEV
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	ROSETTA-GAMI 2(DE3)PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	NEUROPILIN-2 DOMAIN B1 F5/8 TYPE C 1, UNP RESIDUES 275-429
	Gene	:	NRP2, VEGF165R2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2

Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
	Chains	:	F, G, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	SHUFFLE
	Expression System Vector Type	:	PLASMID
	Fragment	:	VEGF-A165-HBD, UNP RESIDUES 205-232
	Gene	:	VEGFA, VEGF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	G
Biological Unit 1 (1x)	:	A						G
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C		E
Biological Unit 4 (1x)	:				D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	DIO	2	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	DIO	-1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DIO	1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	DIO	-1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	DIO	1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET B:274 , VAL C:374 , TYR C:375 , ARG C:376	binding site for residue DIO B 501
2	AC2	SOFTWARE	ARG B:428 , VAL B:429	binding site for residue GOL B 502
3	AC3	SOFTWARE	MET A:274 , VAL D:374 , TYR D:375 , ARG D:376	binding site for residue DIO D 501

Asymmetric Unit

No.	Residues
1	A:277	-	A:427
2	B:277	-	B:427
3	C:277	-	C:427
4	D:277	-	D:427

(no "Cis Peptide Bond" information available for 5DN2)

(no "SAP(SNP)/Variant" information available for 5DN2)

(no "PROSITE Motif" information available for 5DN2)

(no "Exon" information available for 5DN2)

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:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhh.eee.........hhhhh...................eeee....eeeeeeeee...........eeeeeeeeee...........................eeee....eee.eeeeee.eee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dn2 A 274 MFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRV 429
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

Chain B from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhh.eee.........hhhhh...................eeee....eeeeeeeee...........eeeeeeeeee...........................eeee....eee.eeeeee.eee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dn2 B 274 MFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRV 429
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

Chain C from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhh.eee.........hhhhh...................eeee....eeeeeeeee...........eeeeeeeeee................eee........eeee....eee.eeeeee.eee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dn2 C 274 MFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRV 429
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

Chain D from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhh.eee.........hhhhh...................eeee....eeeeeeeee...........eeeeeeeeee...........................eeee....eee.eeeeee.eee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dn2 D 274 MFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRV 429
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 5dn2 E 225 CRCDKPRR 232

Chain F from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5dn2 F 229 KPRR 232

Chain G from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5dn2 G 229 KPRR 232

Legend:		→ Mismatch	(orange background)
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		→ 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 5DN2)

(no "CATH Domain" information available for 5DN2)

(no "Pfam Domain" information available for 5DN2)

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	5dn2
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