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(-) Description

Title :  CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED HETEROCHIRAL {RFX037 PLUS VEGF-A} PROTEIN COMPLEX IN SPACE GROUP P21
 
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. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Heterochiral Protein-Protein Complex, D-Protein Antagonist, Growth Factor-Inhibitor Complex, Racemic 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-PEPTIDE RFX037.D
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - D-VASCULAR ENDOTHELIAL GROWTH FACTOR
    Chains: E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - L-PEPTIDE RFX037.L
    Chains: G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (21, 306)

Asymmetric Unit (21, 306)
No.NameCountTypeFull Name
1DAL10Mod. Amino AcidD-ALANINE
2DAR18Mod. 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
14DSN15Mod. Amino AcidD-SERINE
15DTH26Mod. Amino AcidD-THREONINE
16DTR2Mod. Amino AcidD-TRYPTOPHAN
17DTY14Mod. Amino AcidD-TYROSINE
18DVA22Mod. Amino AcidD-VALINE
19GOL4Ligand/IonGLYCEROL
20MED10Mod. Amino AcidD-METHIONINE
21PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (15, 124)
No.NameCountTypeFull Name
1DAL10Mod. Amino AcidD-ALANINE
2DAR10Mod. Amino AcidD-ARGININE
3DAS16Mod. Amino AcidD-ASPARTIC ACID
4DCY-1Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DGN-1Mod. Amino AcidD-GLUTAMINE
7DHI-1Mod. Amino AcidD-HISTIDINE
8DIL2Mod. Amino AcidD-ISOLEUCINE
9DLE6Mod. Amino AcidD-LEUCINE
10DLY8Mod. Amino AcidD-LYSINE
11DPN14Mod. Amino AcidD-PHENYLALANINE
12DPR-1Mod. Amino AcidD-PROLINE
13DSG4Mod. Amino AcidD-ASPARAGINE
14DSN7Mod. Amino AcidD-SERINE
15DTH20Mod. Amino AcidD-THREONINE
16DTR2Mod. Amino AcidD-TRYPTOPHAN
17DTY6Mod. Amino AcidD-TYROSINE
18DVA10Mod. Amino AcidD-VALINE
19GOL3Ligand/IonGLYCEROL
20MED-1Mod. Amino AcidD-METHIONINE
21PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (19, 182)
No.NameCountTypeFull Name
1DAL-1Mod. Amino AcidD-ALANINE
2DAR8Mod. Amino AcidD-ARGININE
3DAS8Mod. Amino AcidD-ASPARTIC ACID
4DCY16Mod. Amino AcidD-CYSTEINE
5DGL22Mod. Amino AcidD-GLUTAMIC ACID
6DGN12Mod. Amino AcidD-GLUTAMINE
7DHI8Mod. Amino AcidD-HISTIDINE
8DIL16Mod. Amino AcidD-ISOLEUCINE
9DLE8Mod. Amino AcidD-LEUCINE
10DLY10Mod. Amino AcidD-LYSINE
11DPN8Mod. Amino AcidD-PHENYLALANINE
12DPR14Mod. Amino AcidD-PROLINE
13DSG6Mod. Amino AcidD-ASPARAGINE
14DSN8Mod. Amino AcidD-SERINE
15DTH6Mod. Amino AcidD-THREONINE
16DTR-1Mod. Amino AcidD-TRYPTOPHAN
17DTY8Mod. Amino AcidD-TYROSINE
18DVA12Mod. Amino AcidD-VALINE
19GOL1Ligand/IonGLYCEROL
20MED10Mod. Amino AcidD-METHIONINE
21PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (0, 0)

(no "Site" information available for 5HHD)

(-) SS Bonds  (16, 16)

Asymmetric 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  (11, 11)

Asymmetric Unit
No.Residues
1Lys A:41 -Pro A:42
2Pro A:78 -His A:79
3Lys B:41 -Pro B:42
4Gly C:66 -Dsn C:67
5Dar D:3 -Dar D:4
6Dar D:5 -Gly D:6
7Gly D:6 -Gly D:7
8Dly E:41 -Dpr E:42
9Dly F:41 -Dpr F:42
10Arg H:4 -Arg H:5
11Arg H:5 -Gly H:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HHD)

(-) Sequences/Alignments

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:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5hhd 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 .eehhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5hhd B   6 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 100
                                    15        25        35        45        55        65        75        85        95     


Chain C from PDB  Type:PROTEIN  Length:67
                                                                                                   
               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
                 5hhd C   1 xxxxxGGxxxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGx  67
                            |||||  |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     67-DSN
                                    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:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhh.eeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 5hhd D   1 xxxxxGGxxxxxxxxGxxxxGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGG  66
                            |||||  |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      
                                    9-DTH    19-DLE     30-DVA   39-DVA   48-DPN   57-DTH     
                                    10-DTY    20-DLY     31-DPN   40-DTY   49-DAS   58-DLY    


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
                 5hhd E   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 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
                 5hhd F   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 G from PDB  Type:PROTEIN  Length:63
                                                                                               
               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
                 5hhd G   4 RRGGSTYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTEGG  66
                                    13        23        33        43        53        63   


Chain H from PDB  Type:PROTEIN  Length:65
                                                                                                 
               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
                 5hhd H   4 RRGGSTYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTEGGSD  68
                                    13        23        33        43        53        63
   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 5HHD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

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  Cis Peptide Bonds
    Arg H:4 - Arg H:5   [ RasMol ]  
    Arg H:5 - Gly H:6   [ RasMol ]  
    Dar D:3 - Dar D:4   [ RasMol ]  
    Dar D:5 - Gly D:6   [ RasMol ]  
    Dly E:41 - Dpr E:42   [ RasMol ]  
    Dly F:41 - Dpr F:42   [ RasMol ]  
    Gly C:66 - Dsn C:67   [ RasMol ]  
    Gly D:6 - Gly D:7   [ RasMol ]  
    Lys A:41 - Pro A:42   [ RasMol ]  
    Lys B:41 - Pro B:42   [ RasMol ]  
    Pro A:78 - His A:79   [ RasMol ]  
 
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  5hhd
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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 4gls 4kzn 4qaf 4wpb 4zff 5dn2 5fv1 5fv2 5hhc 5t89

(-) Related Entries Specified in the PDB File

4gls 4GLS CONTAINS THE SAME PROTEIN COMPLEXED WITH DIFFERENT D-PROTEIN LIGANDS.