4WPB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH ALPHA/BETA-VEGF-1

Authors :   D. F. Kreitler, J. W. Checco, S. H. Gellman, K. T. Forest

Date :   17 Oct 14 (Deposition) - 15 Apr 15 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.11

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Alpha/Beta-Peptide, Foldamer, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Checco, D. F. Kreitler, N. C. Thomas, D. G. Belair, N. J. Rettko, W. L. Murphy, K. T. Forest, S. H. Gellman
Targeting Diverse Protein-Protein Interaction Interfaces With Alpha / Beta-Peptides Derived From The Z-Domain Scaffold.
Proc. Natl. Acad. Sci. Usa V. 112 4552 2015
PubMed-ID: 25825775 | Reference-DOI: 10.1073/PNAS.1420380112

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	VEGFA, VEGF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF

Molecule 2 - ALPHA/BETA-VEGF-1
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Other Details	:	THIS IS A SYNTHETIC DESIGNED MOLECULE BASED INITIALLY ON THE B DOMAIN OF STAPH AUREUS PROTEIN A.
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 14)

No.	Name	Count	Type	Full Name
1	AIB	4	Mod. Amino Acid	ALPHA-AMINOISOBUTYRIC ACID
2	NH2	2	Mod. Amino Acid	AMINO GROUP
3	XCP	4	Mod. Amino Acid	(1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID
4	XPC	4	Mod. Amino Acid	(3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID

(no "Site" information available for 4WPB)

Asymmetric/Biological 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:10	-	C:39
10	D:10	-	D:39

Asymmetric/Biological Unit

No.	Residues
1	Lys A:48	-	Pro A:49
2	Lys B:48	-	Pro B:49

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

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

(no "Exon" information available for 4WPB)

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
	(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:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh.......ee..eeeeeeee........eeee..eeeeeeeeeeee...eeeeeeeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4wpb A  13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 107
                                    22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeeeeeehhhhh.......ee..eeeeeeee........eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4wpb B  14 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRP 106
                                    23        33        43        53        63        73        83        93       103

Chain C from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 4wpb C   8 ExCNxRAIExALDPNLNDQQFHxKIWxIIxDCx  40
                             |  |   17        27  |   | 37  |
                             9-XCP   |           30-AIB  |  |
                               12-XPC|               34-XPC |
                                    17-AIB              37-XCP
                                                           40-NH2

Chain D from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 4wpb D   8 ExCNxRAIExALDPNLNDQQFHxKIWxIIxDCx  40
                             |  |   17        27  |   | 37  |
                             |  |    |           30-AIB  |  |
                             9-XCP   |               34-XPC |
                               12-XPC|                  37-XCP
                                    17-AIB                 40-NH2

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 4WPB)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		XPC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 4wpb)

	Cis Peptide Bonds
		Lys A:48 - Pro A:49	[ RasMol ]
		Lys B:48 - Pro B:49	[ RasMol ]

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	4wpb
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (0, 0)

SS Bonds (10, 10)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (122, 122)

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