2GNN - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ORF VIRUS NZ2 VARIANT OF VEGF-E

Authors :   A. E. Prota, M. Pieren, A. Wagner, D. Kostrewa, F. K. Winkler, K. Ballmer

Date :   10 Apr 06 (Deposition) - 09 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Vegf, Orf, S-Sad, , Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Pieren, A. E. Prota, C. Ruch, D. Kostrewa, A. Wagner, K. Biedermann, F. K. Winkler, K. Ballmer-Hofer
Crystal Structure Of The Orf Virus Nz2 Variant Of Vascular Endothelial Growth Factor-E. Implications For Receptor Specificity.
J. Biol. Chem. V. 281 19578 2006
PubMed-ID: 16672228 | Reference-DOI: 10.1074/JBC.M601842200
(for further references see the PDB file header)

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR HOMOLOG
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZALPHA
	Expression System Strain	:	X33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ORF VIRUS (STRAIN NZ2)
	Organism Taxid	:	10259
	Strain	:	NZ2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 20)

No.	Name	Count	Type	Full Name
1	BEN	3	Ligand/Ion	BENZAMIDINE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	GOL	8	Ligand/Ion	GLYCEROL
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	2	Ligand/Ion	SULFATE ION
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (5, 12)

No.	Name	Count	Type	Full Name
1	BEN	2	Ligand/Ion	BENZAMIDINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	7	Ligand/Ion	GLYCEROL
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	1	Ligand/Ion	SULFATE ION
6	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	BEN	1	Ligand/Ion	BENZAMIDINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	1	Ligand/Ion	SULFATE ION
6	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (5, 17)

No.	Name	Count	Type	Full Name
1	BEN	3	Ligand/Ion	BENZAMIDINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	8	Ligand/Ion	GLYCEROL
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	2	Ligand/Ion	SULFATE ION
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:75 , THR C:38 , ARG C:56 , SER C:95 , PHE C:96 , VAL C:97	BINDING SITE FOR RESIDUE NAG B 1001
02	AC2	SOFTWARE	THR A:38 , ARG A:56 , PHE A:96 , VAL A:97 , GLU D:73 , ASN D:75	BINDING SITE FOR RESIDUE NAG D 1002
03	AC3	SOFTWARE	ARG C:107	BINDING SITE FOR RESIDUE CL C 704
04	AC4	SOFTWARE	SER C:18	BINDING SITE FOR RESIDUE CL C 705
05	AC5	SOFTWARE	ARG A:107	BINDING SITE FOR RESIDUE CL A 702
06	AC6	SOFTWARE	SER B:84 , GLY B:85 , GOL B:608 , LYS C:101	BINDING SITE FOR RESIDUE SO4 C 500
07	AC7	SOFTWARE	LYS A:101 , SER D:84 , GLY D:85 , SER D:86	BINDING SITE FOR RESIDUE SO4 A 501
08	AC8	SOFTWARE	LEU A:66 , ASP A:103 , CYS A:104 , ARG A:105 , SER D:44 , GLY D:85 , SER D:86 , GLY D:87	BINDING SITE FOR RESIDUE BEN A 1001
09	AC9	SOFTWARE	SER B:44 , GLY B:85 , SER B:86 , GLY B:87 , LEU C:66 , ASP C:103 , CYS C:104 , ARG C:105	BINDING SITE FOR RESIDUE BEN B 1002
10	BC1	SOFTWARE	GLU A:64 , GOL A:606 , ARG B:46 , GLU C:64 , ARG D:46 , HOH D:1046 , HOH D:1047	BINDING SITE FOR RESIDUE BEN D 1003
11	BC2	SOFTWARE	ASP A:63 , GLU A:64 , SER D:44 , GLN D:45 , ARG D:46	BINDING SITE FOR RESIDUE TRS A 900
12	BC3	SOFTWARE	SER B:44 , GLN B:45 , ASP C:63 , GLU C:64 , SER C:65	BINDING SITE FOR RESIDUE TRS C 901
13	BC4	SOFTWARE	LYS A:22 , LYS A:27 , HOH A:1028	BINDING SITE FOR RESIDUE GOL A 601
14	BC5	SOFTWARE	GLY A:16 , TRP A:17 , SER A:18 , GLU A:19	BINDING SITE FOR RESIDUE GOL A 602
15	BC6	SOFTWARE	GLU C:73 , HIS C:99	BINDING SITE FOR RESIDUE GOL C 603
16	BC7	SOFTWARE	GLU A:79 , GLY B:16 , TRP B:17 , SER B:18	BINDING SITE FOR RESIDUE GOL B 604
17	BC8	SOFTWARE	GLU A:64 , ARG B:46 , BEN D:1003	BINDING SITE FOR RESIDUE GOL A 606
18	BC9	SOFTWARE	SER B:84 , SER B:86 , HOH B:1046 , GLU C:25 , CYS C:26 , SO4 C:500	BINDING SITE FOR RESIDUE GOL B 608
19	CC1	SOFTWARE	GLU B:73 , VAL B:97 , HIS B:99 , HOH B:1047	BINDING SITE FOR RESIDUE GOL B 609
20	CC2	SOFTWARE	ASN A:13 , LYS A:15 , LYS B:100 , HOH B:1035	BINDING SITE FOR RESIDUE GOL A 610

Asymmetric Unit

No.	Residues
1	A:26	-	A:68
2	A:51	-	B:60
3	A:57	-	A:102
4	A:60	-	B:51
5	A:61	-	A:104
6	B:26	-	B:68
7	B:57	-	B:102
8	B:61	-	B:104
9	C:26	-	C:68
10	C:51	-	D:60
11	C:57	-	C:102
12	C:60	-	D:51
13	C:61	-	C:104
14	D:26	-	D:68
15	D:57	-	D:102
16	D:61	-	D:104

Asymmetric Unit

No.	Residues
1	Asn A:48	-	Pro A:49
2	Asn B:48	-	Pro B:49
3	Asn C:48	-	Pro C:49
4	Asn D:48	-	Pro D:49

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

Asymmetric Unit (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDGF_2	PS50278	Platelet-derived growth factor (PDGF) family profile.	VEGFH_ORFN2	23-119	3	A:13-109 B:13-107 C:13-109
2	PDGF_1	PS00249	Platelet-derived growth factor (PDGF) family signature.	VEGFH_ORFN2	59-71	4	A:49-61 B:49-61 C:49-61 D:49-61

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDGF_2	PS50278	Platelet-derived growth factor (PDGF) family profile.	VEGFH_ORFN2	23-119	2	A:13-109 B:13-107 -
2	PDGF_1	PS00249	Platelet-derived growth factor (PDGF) family signature.	VEGFH_ORFN2	59-71	2	A:49-61 B:49-61 - -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDGF_2	PS50278	Platelet-derived growth factor (PDGF) family profile.	VEGFH_ORFN2	23-119	1	- - C:13-109
2	PDGF_1	PS00249	Platelet-derived growth factor (PDGF) family signature.	VEGFH_ORFN2	59-71	2	- - C:49-61 D:49-61

Biological Unit 3 (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDGF_2	PS50278	Platelet-derived growth factor (PDGF) family profile.	VEGFH_ORFN2	23-119	3	A:13-109 B:13-107 C:13-109
2	PDGF_1	PS00249	Platelet-derived growth factor (PDGF) family signature.	VEGFH_ORFN2	59-71	4	A:49-61 B:49-61 C:49-61 D:49-61

(no "Exon" information available for 2GNN)

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:92
 aligned with VEGFH_ORFN2 | P52584 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:99
                                    30        40        50        60        70        80        90       100       110         
          VEGFH_ORFN2    21 DSNTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVSMELLGASGSGSNGMQRLSFVEHKKCDCRPRFT 119
               SCOP domains d2gnna_ A: automated matches                                                                        SCOP domains
               CATH domains 2gnnA00 A:11-109 Cystine-knot cytokines                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhh.eeeeeeee.hhh............eeeeeeee.......eeeeeeeeeeeeeee..-------..eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDGF_2  PDB: A:13-109 UniProt: 23-119                                                             PROSITE (1)
                PROSITE (2) --------------------------------------PDGF_1       ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2gnn A  11 DSNTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVTMELLG-------GMQRLSFVEHKKCDCRPRFT 109
                                    20        30        40        50        60        70        80 |      90       100         
                                                                                                  82      90

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with VEGFH_ORFN2 | P52584 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:95
                                    32        42        52        62        72        82        92       102       112     
          VEGFH_ORFN2    23 NTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVSMELLGASGSGSNGMQRLSFVEHKKCDCRPR 117
               SCOP domains d2gnnb_ B: automated matches                                                                    SCOP domains
               CATH domains 2gnnB00 B:13-107 Cystine-knot cytokines                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh...........eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: B:13-107 UniProt: 23-119                                                           PROSITE (1)
                PROSITE (2) ------------------------------------PDGF_1       ---------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2gnn B  13 NTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVTMELLGASGSGSNGMQRLSFVEHKKCDCRPR 107
                                    22        32        42        52        62        72        82        92       102

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with VEGFH_ORFN2 | P52584 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:100
                                    30        40        50        60        70        80        90       100       110       120
          VEGFH_ORFN2    21 DSNTKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVSMELLGASGSGSNGMQRLSFVEHKKCDCRPRFTT 120
               SCOP domains d2gnnc_ C: automated matches                                                                         SCOP domains
               CATH domains 2gnnC00 C:11-110 Cystine-knot c  ytokines                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhh.eeeeeeeehhhhh..--.......eeeeeeee.......eeeeeeeeeeeeeee..--------.eeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDGF_2  PDB: C:13-109 UniProt: 23-119                                                            - PROSITE (1)
                PROSITE (2) --------------------------------------PDGF_1       ------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2gnn C  11 DSNTKGWSEVLKGSECKPRPIVVPVSETHPE--SQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVTMELLG--------MQRLSFVEHKKCDCRPRFTT 110
                                    20        30        40|  |    50        60        70        80 |       -|      100       110
                                                         41 44                                    82       91

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with VEGFH_ORFN2 | P52584 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:93
                                    33        43        53        63        73        83        93       103       113   
          VEGFH_ORFN2    24 TKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVSMELLGASGSGSNGMQRLSFVEHKKCDCRP 116
               SCOP domains d2gnnd_ D: automated matches                                                                  SCOP domains
               CATH domains 2gnnD00 D:14-106 Cystine-knot cytokines                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..eeeeeeeehhhhh...........eeeeeeee.........eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: - UniProt: 23-119                                                                PROSITE (1)
                PROSITE (2) -----------------------------------PDGF_1       --------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 2gnn D  14 TKGWSEVLKGSECKPRPIVVPVSETHPELTSQRFNPPCVTLMRCGGCCNDESLECVPTEEVNVTMELLGASGSGSNGMQRLSFVEHKKCDCRP 106
                                    23        33        43        53        63        73        83        93       103

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Cystine-knot cytokines (124)

Superfamily: Cystine-knot cytokines (124)

Family: automated matches (18)

Protein domain: automated matches (18)

Orf virus [TaxId: 10259] (1)

1a	d2gnna_	A:
1b	d2gnnb_	B:
1c	d2gnnc_	C:
1d	d2gnnd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cystine Knot Cytokines, subunit B (102)

Homologous Superfamily: Cystine-knot cytokines (102)

Orf virus (strain nz2). Organism_taxid: 10259. Strain: nz2. (1)

1a	2gnnB00	B:13-107
1b	2gnnD00	D:14-106
1c	2gnnA00	A:11-109
1d	2gnnC00	C:11-110

(no "Pfam Domain" information available for 2GNN)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (VEGFH_ORFN2 | P52584)

molecular function
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
biological process
	GO:0051781	positive regulation of cell division	Any process that activates or increases the frequency, rate or extent of cell division.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:48 - Pro A:49	[ RasMol ]
		Asn B:48 - Pro B:49	[ RasMol ]
		Asn C:48 - Pro C:49	[ RasMol ]
		Asn D:48 - Pro D:49	[ RasMol ]

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	2gnn
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	VEGFH_ORFN2 \| P52584
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	VEGFH_ORFN2 \| P52584
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	VEGFH_ORFN2 \| P52584	:	3v6b

1fzv	THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 (PLGF-1), AN ANGIOGENIC PROTEIN AT 2.0A RESOLUTION
1vpf	STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR
1wq8	CRYSTAL STRUCTURE OF VAMMIN, A VEGF-F FROM A SNAKE VENOM
1wq9	CRYSTAL STRUCTURE OF VR-1, A VEGF-F FROM A SNAKE VENOM

Description

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Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (20, 20)

SS Bonds (16, 16)

Cis Peptide Bonds (4, 4)

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