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(-) Description

Title :  CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED HETEROCHIRAL {D-PROTEIN ANTAGONIST PLUS VEGF-A} PROTEIN COMPLEX IN SPACE GROUP P21
 
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 :  A,B,C,D,E,F,G,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- VASCULAR ENDOTHELIAL GROWTH FACTOR-A
    Chains: A, B
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 2 - L- RFX001
    Chains: C, G
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - D- RFX001
    Chains: D, H
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 4 - 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

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (21, 290)

Asymmetric/Biological Unit (21, 290)
No.NameCountTypeFull Name
1DAL10Mod. Amino AcidD-ALANINE
2DAR8Mod. Amino AcidD-ARGININE
3DAS24Mod. Amino AcidD-ASPARTIC ACID
4DCY16Mod. Amino AcidD-CYSTEINE
5DGL28Mod. Amino AcidD-GLUTAMIC ACID
6DGN12Mod. Amino AcidD-GLUTAMINE
7DHI8Mod. Amino AcidD-HISTIDINE
8DIL18Mod. Amino AcidD-ISOLEUCINE
9DLE14Mod. Amino AcidD-LEUCINE
10DLY18Mod. Amino AcidD-LYSINE
11DPN22Mod. Amino AcidD-PHENYLALANINE
12DPR14Mod. Amino AcidD-PROLINE
13DSG10Mod. Amino AcidD-ASPARAGINE
14DSN12Mod. Amino AcidD-SERINE
15DTH26Mod. Amino AcidD-THREONINE
16DTR2Mod. Amino AcidD-TRYPTOPHAN
17DTY14Mod. Amino AcidD-TYROSINE
18DVA22Mod. Amino AcidD-VALINE
19GOL1Ligand/IonGLYCEROL
20MED10Mod. Amino AcidD-METHIONINE
21PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDPN A:29 , DGL A:35 , DIL A:36 , DGL A:37 , DTY A:38BINDING SITE FOR RESIDUE PEG A 201
2AC2SOFTWAREGLY E:52 , LEU F:25 , HOH F:313 , HOH F:369BINDING SITE FOR RESIDUE GOL F 201

(-) SS Bonds  (16, 16)

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
9E:19 -E:61
10E:44 -F:53
11E:50 -E:95
12E:53 -F:44
13E:54 -E:97
14F:19 -F:61
15F:50 -F:95
16F:54 -F:97

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Dly A:41 -Dpr A:42
2Dly B:41 -Dpr B:42
3Lys E:41 -Pro E:42
4Lys F:41 -Pro F:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GLS)

(-) 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
                 4gls A   6 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGxxxxxGxxxxxxxxxxxxxxxxxxxxxxGxxxGxxxxxxxxxxxxxxx 100
                            ||||||||15||||||||25||||||||35||||||||45|||||  |55|| |||||65||||||||75||||| ||85||||||||95|||||
                            |||||||14-DTY|||23-DGL|||32-DTY|||41-DLY|||50-DCY||| ||62-DVA|||71-MED|||80-DGN ||||91-DGN||100-DLY
                            6-DGL|||15-DGN|||24-DTH|||33-DPR|||42-DPR|||  53-DCY |||63-DPR|||72-DGN||| 82-DGN||||92-DHI||| 
                             7-DVA|| 16-DAR|| 25-DLE|| 34-DAS|| 43-DSN||   54-DCY||| 64-DTH|| 73-DIL||  83-DHI||| 93-DSG|| 
                              8-DVA|  17-DSN|  26-DVA|  35-DGL|  44-DCY|    55-DSG||  65-DGL|  74-MED|   84-DIL||  94-DLY| 
                               9-DLY   18-DTY   27-DAS   36-DIL   45-DVA     56-DAS|   66-DGL   75-DAR     86-DGL   95-DCY 
                               10-DPN   19-DCY   28-DIL   37-DGL   46-DPR     57-DGL    67-DSN   76-DIL     87-MED   96-DGL
                                11-MED   20-DHI   29-DPN   38-DTY   47-DLE      59-DLE   68-DSG   77-DLY     88-DSN   97-DCY
                                 12-DAS   21-DPR   30-DGN   39-DIL   48-MED      60-DGL   69-DIL   78-DPR     89-DPN   98-DAR
                                  13-DVA   22-DIL   31-DGL   40-DPN   49-DAR      61-DCY   70-DTH   79-DHI     90-DLE   99-DPR


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
                 4gls B   6 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGxxxxxGxxxxxxxxxxxxxxxxxxxxxxGxxxGxxxxxxxxxxxxxxx 100
                            ||||||||15||||||||25||||||||35||||||||45|||||  |55|| |||||65||||||||75||||| ||85||||||||95|||||
                            |||||||14-DTY|||23-DGL|||32-DTY|||41-DLY|||50-DCY||| ||62-DVA|||71-MED|||80-DGN ||||91-DGN||100-DLY
                            6-DGL|||15-DGN|||24-DTH|||33-DPR|||42-DPR|||  53-DCY |||63-DPR|||72-DGN||| 82-DGN||||92-DHI||| 
                             7-DVA|| 16-DAR|| 25-DLE|| 34-DAS|| 43-DSN||   54-DCY||| 64-DTH|| 73-DIL||  83-DHI||| 93-DSG|| 
                              8-DVA|  17-DSN|  26-DVA|  35-DGL|  44-DCY|    55-DSG||  65-DGL|  74-MED|   84-DIL||  94-DLY| 
                               9-DLY   18-DTY   27-DAS   36-DIL   45-DVA     56-DAS|   66-DGL   75-DAR     86-DGL   95-DCY 
                               10-DPN   19-DCY   28-DIL   37-DGL   46-DPR     57-DGL    67-DSN   76-DIL     87-MED   96-DGL
                                11-MED   20-DHI   29-DPN   38-DTY   47-DLE      59-DLE   68-DSG   77-DLY     88-DSN   97-DCY
                                 12-DAS   21-DPR   30-DGN   39-DIL   48-MED      60-DGL   69-DIL   78-DPR     89-DPN   98-DAR
                                  13-DVA   22-DIL   31-DGL   40-DPN   49-DAR      61-DCY   70-DTH   79-DHI     90-DLE   99-DPR


Chain C 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.eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4gls C   1 TYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTE  56
                                    10        20        30        40        50      


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
                 4gls D   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


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


Chain G from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeee...hhhhhhhhhhhhhhh...ee.eeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4gls G   1 TYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTE  56
                                    10        20        30        40        50      


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...hhhhhhhhhhhhhhh...ee.eeeeehhh.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4gls 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)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4GLS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  VEGFA_HUMAN | P15692
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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 4kzn 4qaf 4wpb 4zff 5dn2 5fv1 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

3qtk 4gln 4glu