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(-) Description

Title :  CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED HETEROCHIRAL {D-PROTEIN ANTAGONIST PLUS VEGF-A} PROTEIN COMPLEX IN SPACE GROUP P21/N
 
Authors :  K. Mandal, M. Uppalapati, D. Ault-Riche, J. Kenney, J. Lowitz, S. Sidhu S. B. H. Kent
Date :  14 Aug 12  (Deposition) - 05 Sep 12  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  D,E,F,H
Keywords :  Heterochiral Protein-Protein Complex, D-Protein Antagonist, Growth Factor-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mandal, M. Uppalapati, D. Ault-Riche, J. Kenney, J. Lowitz, S. S. Sidhu, S. B. Kent
Chemical Synthesis And X-Ray Structure Of A Heterochiral {D-Protein Antagonist Plus Vascular Endothelial Growth Factor} Protein Complex By Racemic Crystallography.
Proc. Natl. Acad. Sci. Usa V. 109 14779 2012
PubMed-ID: 22927390  |  Reference-DOI: 10.1073/PNAS.1210483109

(-) Compounds

Molecule 1 - D-RFX001
    Chains: D, H
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: E, F
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : DEFH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (13, 108)

Asymmetric/Biological Unit (13, 108)
No.NameCountTypeFull Name
1DAL10Mod. Amino AcidD-ALANINE
2DAS16Mod. Amino AcidD-ASPARTIC ACID
3DGL6Mod. Amino AcidD-GLUTAMIC ACID
4DIL2Mod. Amino AcidD-ISOLEUCINE
5DLE6Mod. Amino AcidD-LEUCINE
6DLY8Mod. Amino AcidD-LYSINE
7DPN14Mod. Amino AcidD-PHENYLALANINE
8DSG4Mod. Amino AcidD-ASPARAGINE
9DSN4Mod. Amino AcidD-SERINE
10DTH20Mod. Amino AcidD-THREONINE
11DTR2Mod. Amino AcidD-TRYPTOPHAN
12DTY6Mod. Amino AcidD-TYROSINE
13DVA10Mod. Amino AcidD-VALINE

(-) Sites  (0, 0)

(no "Site" information available for 4GLN)

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys E:41 -Pro E:42
2Lys F:41 -Pro F:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GLN)

(-) 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 D from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.ee.eeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4gln D   1 xxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  56
                            ||||||| 10|| |||||20||||||||30||||||||40||||||||50||||||
                            ||||||| 10-DTH||||20-DVA|||29-DPN|||38-DSN|||47-DAS|||56-DGL
                            1-DTH|| |11-DLE||||21-DAS|||30-DPN|||39-DAS|||48-DAL||| 
                             2-DTY| | 12-DLY||| 22-DVA|| 31-DVA|| 40-DPN|| 49-DTH|| 
                              3-DLY |   14-DGL|  23-DPN|  32-DTY|  41-DAS|  50-DLY| 
                               4-DLE|    15-DTH   24-DAS   33-DAL   42-DAS   51-DTH 
                                5-DIL     16-DTH   25-DAL   34-DAL   43-DTR   52-DPN
                                 6-DLE     17-DTH   26-DPN   35-DSN   44-DTH   53-DTH
                                  7-DSG     18-DGL   27-DAS   36-DSG   45-DTY   54-DVA
                                    9-DLY    19-DAL   28-DVA   37-DPN   46-DAS   55-DTH


Chain E 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
                 4gln E   6 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 100
                                    15        25        35        45        55        65        75        85        95     


Chain F 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
                 4gln F   6 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 100
                                    15        25        35        45        55        65        75        85        95     


Chain H from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.ee.eeeeehhh.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4gln H   1 xxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  56
                            ||||||| 10|| |||||20||||||||30||||||||40||||||||50||||||
                            1-DTH|| |11-DLE||||21-DAS|||30-DPN|||39-DAS|||48-DAL||||
                             2-DTY| ||12-DLY||||22-DVA|||31-DVA|||40-DPN|||49-DTH|||
                              3-DLY ||  14-DGL|| 23-DPN|| 32-DTY|| 41-DAS|| 50-DLY||
                               4-DLE||   15-DTH|  24-DAS|  33-DAL|  42-DAS|  51-DTH|
                                5-DIL|    16-DTH   25-DAL   34-DAL   43-DTR   52-DPN
                                 6-DLE     17-DTH   26-DPN   35-DSN   44-DTH   53-DTH
                                  7-DSG     18-DGL   27-DAS   36-DSG   45-DTY   54-DVA
                                    9-DLY    19-DAL   28-DVA   37-DPN   46-DAS   55-DTH
                                    10-DTH    20-DVA   29-DPN   38-DSN   47-DAS   56-DGL
   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 4GLN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4gls 4kzn 4qaf 4wpb 4zff 5dn2 5fv1 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

3qtk 4gls 4glu