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(-) Description

Title :  STRUCTURE OF A COMPUTATIONALLY DESIGNED 17-OHP BINDER
 
Authors :  B. L. Stoddard, L. A. Doyle
Date :  25 Feb 16  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Rossetta, Ligand Binder, Computational, Structural Genomics, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Stoddard
Tbd
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OHP9_1C
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
13QZ6Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:12 , THR A:16 , PHE A:107 , TYR A:124 , HOH A:301 , HOH A:302 , PHE F:99binding site for residue 3QZ A 201
2AC2SOFTWARESER A:9binding site for residue NA A 202
3AC3SOFTWARELEU B:12 , THR B:16 , ALA B:91 , PHE B:107 , TYR B:124 , HOH B:301 , HOH B:303 , PHE E:99binding site for residue 3QZ B 201
4AC4SOFTWARESER B:9binding site for residue NA B 202
5AC5SOFTWARELEU C:12 , GLY C:13 , THR C:16 , ALA C:91 , PHE C:107 , TYR C:124 , PHE D:99binding site for residue 3QZ C 201
6AC6SOFTWAREPHE C:99 , THR D:16 , TRP D:24 , THR D:43 , VAL D:103 , PHE D:107 , TYR D:124binding site for residue 3QZ D 201
7AC7SOFTWAREPHE B:99 , GLY E:13 , THR E:16 , THR E:43 , ALA E:91 , PHE E:107 , TYR E:124binding site for residue 3QZ E 201
8AC8SOFTWARELEU F:12 , THR F:16 , THR F:43 , VAL F:71 , PHE F:107 , TYR F:124 , HOH F:301binding site for residue 3QZ F 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IF6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:36 -Pro A:37
2Thr B:36 -Pro B:37
3Thr C:36 -Pro C:37
4Thr D:36 -Pro D:37
5Thr E:36 -Pro E:37
6Thr F:36 -Pro F:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IF6)

(-) Exons   (0, 0)

(no "Exon" information available for 5IF6)

(-) 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:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeeeee...eeeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 A   1 TQSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEFDGGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 B   2 QSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEFDGGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   


Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 C   1 TQSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEFDGGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain D from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeeeee...eeeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 D   1 TQSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEFDGGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain E from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 E   1 TQSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEFDGGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain F from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeeeee...eeeeeeeeeeee.....eeeeeee.hhhhheee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5if6 F   1 TQSPALIASQSLGRCTQAKDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFWDTHIADDRVTVTCEETFPSSSPDEIAHILVAHAEGFTSEVRGVFTYRVNKAGLITNLRGYYNLDMMTFGNQ 134
                                    10        20        30        40        50        60        70        80        90   ||  103       113       123       133 
                                                                                                                        94|                                    
                                                                                                                         98
   Legend:   → Mismatch (orange background)
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  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 5IF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IF6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5IF6)

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5ien 5ieo 5iep 5ier