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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 :  2.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rossetta, Ligand Binder, Computational, Structural Genomics, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Stoddard, L. A. Doyle
Tbd
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OHP9
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: COMPUTATIONAL DESIGN
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
13QZ4Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA4Ligand/IonSODIUM ION
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
13QZ1Ligand/Ion(9BETA)-17-HYDROXYPREGN-4-ENE-3,20-DIONE
2NA-1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:12 , TRP A:13 , THR A:16 , THR A:43 , HIS A:63 , LEU A:69 , SER A:93 , PHE A:107 , TYR A:109binding site for residue 3QZ A 201
02AC2SOFTWAREARG A:68 , HIS C:19 , ARG C:68binding site for residue SO4 A 202
03AC3SOFTWAREARG A:110 , ASN A:112 , NA A:204 , NA A:205 , HOH A:341 , HOH A:355 , ALA B:114binding site for residue SO4 A 203
04AC4SOFTWARESO4 A:203 , ALA B:114 , HOH B:365binding site for residue NA A 204
05AC5SOFTWAREASN A:112 , LYS A:113 , SO4 A:203 , HOH A:362 , ALA B:114 , LEU B:116binding site for residue NA A 205
06AC6SOFTWARELEU B:12 , TRP B:13 , THR B:16 , THR B:43 , LEU B:69 , ALA B:91 , PHE B:107 , HOH B:323 , HOH B:357binding site for residue 3QZ B 201
07AC7SOFTWAREARG B:110 , THR B:118 , HOH B:361binding site for residue SO4 B 202
08AC8SOFTWARELEU C:12 , TRP C:13 , THR C:36 , THR C:43 , LEU C:89 , ALA C:91 , SER C:93 , TYR C:109 , TRP C:124binding site for residue 3QZ C 201
09AC9SOFTWAREARG C:110 , THR C:118 , HOH C:341binding site for residue SO4 C 202
10AD1SOFTWARELEU D:12 , TRP D:13 , THR D:16 , THR D:43 , VAL D:103 , HOH D:310 , HOH D:325binding site for residue 3QZ D 201
11AD2SOFTWAREARG D:110 , THR D:118 , NA D:203 , NA D:204binding site for residue SO4 D 202
12AD3SOFTWAREASN D:112 , LYS D:113 , SO4 D:202binding site for residue NA D 203
13AD4SOFTWAREASP D:31 , ASN D:112 , SO4 D:202binding site for residue NA D 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IER)

(-) 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:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh..eeeeeeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee.....eeeeeee.hhhhheee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ier A   2 QSPALIASQSLWRCTQAHDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFFDTHIAATRLTVTCEETFPSSSPDEIAHILVAHSEFDGGFTSEVRGVFTYRVNKAGLITNLRGYWNLDMMTFG 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh...eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeeee.....eeeeeee......eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ier B   2 QSPALIASQSLWRCTQAHDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFFDTHIAATRLTVTCEETFPSSSPDEIAHILVAHSEFDGGFTSEVRGVFTYRVNKAGLITNLRGYWNLDMMTFG 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 


Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee..............eehhhhhhhhhhhhh..eeeeeeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee.....eeeeeee.hhh.eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ier C   2 QSPALIASQSLWRCTQAHDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFFDTHIAATRLTVTCEETFPSSSPDEIAHILVAHSEFDGGFTSEVRGVFTYRVNKAGLITNLRGYWNLDMMTFG 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhheeeeeeee..............eehhhhhhhhhhhhh...eeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeee.....eeeeeee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ier D   2 QSPALIASQSLWRCTQAHDREGWLALMADDVVIETPIGKSVTNPDGSGIKGKEAVGAFFDTHIAATRLTVTCEETFPSSSPDEIAHILVAHSEFTSEVRGVFTYRVNKAGLITNLRGYWNLDMMTF 131
                                    11        21        31        41        51        61        71        81        91  ||   105       115       125      
                                                                                                                       94|                                
                                                                                                                        99
   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 5IER)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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(-) Related Entries Specified in the PDB File

5ien 5ieo 5iep 5if6