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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED HETEROCHIRAL {RFX037 PLUS VEGF-A} PROTEIN COMPLEX IN SPACE GROUP P21/N
 
Authors :  M. Uppalapati, D. J. Lee, K. Mandal, S. B. H. Kent, S. Sidhu
Date :  10 Jan 16  (Deposition) - 09 Mar 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Heterochiral Protein-Protein Complex, D-Protein Antagonist, Growth Factor-Inhibitor Complex, Racemic Protein Crystallography, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Uppalapati, D. J. Lee, K. Mandal, H. Li, L. P. Miranda, J. Lowitz, J. Kenney, J. J. Adams, D. Ault-Riche, S. B. Kent, S. S. Sidhu
A Potent D-Protein Antagonist Of Vegf-A Is Nonimmunogenic, Metabolically Stable, And Longer-Circulating In Vivo.
Acs Chem. Biol. V. 11 1058 2016
PubMed-ID: 26745345  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B01006

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: A, B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHEMICAL SYNTHESIS
    Synonym: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF
    Synthetic: YES
 
Molecule 2 - D- VASCULAR ENDOTHELIAL GROWTH FACTOR-A
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (15, 124)

Asymmetric/Biological Unit (15, 124)
No.NameCountTypeFull Name
1DAL10Mod. Amino AcidD-ALANINE
2DAR10Mod. Amino AcidD-ARGININE
3DAS17Mod. Amino AcidD-ASPARTIC ACID
4DGL6Mod. Amino AcidD-GLUTAMIC ACID
5DIL2Mod. Amino AcidD-ISOLEUCINE
6DLE6Mod. Amino AcidD-LEUCINE
7DLY8Mod. Amino AcidD-LYSINE
8DPN14Mod. Amino AcidD-PHENYLALANINE
9DSG4Mod. Amino AcidD-ASPARAGINE
10DSN7Mod. Amino AcidD-SERINE
11DTH20Mod. Amino AcidD-THREONINE
12DTR2Mod. Amino AcidD-TRYPTOPHAN
13DTY6Mod. Amino AcidD-TYROSINE
14DVA10Mod. Amino AcidD-VALINE
15GOL2Ligand/IonGLYCEROL

(-) Sites  (0, 0)

(no "Site" information available for 5HHC)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:61
2A:44 -B:53
3A:50 -A:95
4A:53 -B:44
5A:54 -A:97
6B:19 -B:61
7B:50 -B:95
8B:54 -B:97

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:41 -Pro A:42
2Lys B:41 -Pro B:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HHC)

(-) Sequences/Alignments

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......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5hhc A   6 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 100
                                    15        25        35        45        55        65        75        85        95     


Chain B from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5hhc B   6 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 100
                                    15        25        35        45        55        65        75        85        95     


Chain C from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhh...eeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5hhc C   1 xxxxxGGxxxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGG  66
                            |||||  |10||||| ||20 |||||||30||||||||40||||||||50||||||||60||||  
                            1-DAR  |||12-DLE|||| 23-DTH|||32-DAS|||41-DAL|||50-DAS|||59-DTH|  
                             2-DAR ||||13-DIL||| |24-DTH|||33-DAL|||42-DAL|||51-DTR|||60-DPN  
                              3-DAR|||| 14-DLE|| | 25-DTH|| 34-DPN|| 43-DSN|| 52-DTH|| 61-DTH 
                               4-DAR|||  15-DSG| |  26-DGL|  35-DAS|  44-DSG|  53-DTY|  62-DVA
                                5-DAR||    17-DLY|   27-DAL   36-DVA   45-DPN   54-DAS   63-DTH
                                   8-DSN    18-DTH    28-DVA   37-DPN   46-DSN   55-DAS   64-DGL
                                    9-DTH    19-DLE    29-DAS   38-DPN   47-DAS   56-DAL      
                                    10-DTY    20-DLY    30-DVA   39-DVA   48-DPN   57-DTH     
                                     11-DLY     22-DGL   31-DPN   40-DTY   49-DAS   58-DLY    


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 5hhc D   1 xxxxxGGxxxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGxx  68
                            |||||  |10||||| ||20 |||||||30||||||||40||||||||50||||||||60||||  ||
                            |||||  ||11-DLY |||| 23-DTH|||32-DAS|||41-DAL|||50-DAS|||59-DTH|  ||
                            1-DAR  |||12-DLE|||| |24-DTH|||33-DAL|||42-DAL|||51-DTR|||60-DPN  ||
                             2-DAR ||| 13-DIL||| | 25-DTH|| 34-DPN|| 43-DSN|| 52-DTH|| 61-DTH ||
                              3-DAR|||  14-DLE|| |  26-DGL|  35-DAS|  44-DSG|  53-DTY|  62-DVA||
                               4-DAR||   15-DSG| |   27-DAL   36-DVA   45-DPN   54-DAS   63-DTH|
                                5-DAR|     17-DLY|    28-DVA   37-DPN   46-DSN   55-DAS   64-DGL
                                   8-DSN    18-DTH     29-DAS   38-DPN   47-DAS   56-DAL     67-DSN
                                    9-DTH    19-DLE     30-DVA   39-DVA   48-DPN   57-DTH     68-DAS
                                    10-DTY    20-DLY     31-DPN   40-DTY   49-DAS   58-DLY
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HHC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VEGFA_HUMAN | P15692: 1bj1 1cz8 1flt 1kat 1kmx 1mjv 1mkg 1mkk 1qty 1tzh 1tzi 1vgh 1vpf 1vpp 2fjg 2fjh 2qr0 2vgh 2vpf 3bdy 3p9w 3qtk 3s1b 3s1k 3v2a 4deq 4gln 4gls 4kzn 4qaf 4wpb 4zff 5dn2 5fv1 5fv2 5hhd 5t89

(-) Related Entries Specified in the PDB File

4gln 4GLN CONTAINS THE SAME PROTEIN COMPLEXED WITH SIMILAR D-PROTEIN LIGAND