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(-) Description

Title :  GRB7 SH2 WITH THE G7-B1 BICYCLIC PEPTIDE INHIBITOR
 
Authors :  N. D. Ambaye, G. M. Watson, M. C. J. Wilce, G. M. Wilce
Date :  23 Oct 15  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,L,M
Biol. Unit 1:  A,L  (1x)
Biol. Unit 2:  B,M  (1x)
Keywords :  Staple, Sh2, Inhibitor, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Gunzburg, K. Kulkarni, G. M. Watson, N. D. Ambaye, M. P. Del Borgo R. Brandt, S. C. Pero, P. Perlmutter, M. C. Wilce, J. A. Wilce
Unexpected Involvement Of Staple Leads To Redesign Of Selective Bicyclic Peptide Inhibitor Of Grb7.
Sci Rep V. 6 27060 2016
PubMed-ID: 27257138  |  Reference-DOI: 10.1038/SREP27060

(-) Compounds

Molecule 1 - GROWTH FACTOR RECEPTOR-BOUND PROTEIN 7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RERSIDUES 415-532
    GeneGRB7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymB47,EPIDERMAL GROWTH FACTOR RECEPTOR GRB-7,GRB7 ADAPTER PROTEIN
 
Molecule 2 - BICYCLIC PEPTIDE INHIBITOR
    ChainsL, M
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABLM
Biological Unit 1 (1x)A L 
Biological Unit 2 (1x) B M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
148V2Mod. Amino Acid{[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID
273C2Mod. Amino Acid(2~{S})-2-AZANYL-3-BUTOXY-PROPANOIC ACID
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
148V1Mod. Amino Acid{[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID
273C1Mod. Amino Acid(2~{S})-2-AZANYL-3-BUTOXY-PROPANOIC ACID
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
148V1Mod. Amino Acid{[(2R)-2,3-DIAMINO-3-OXOPROPYL]SULFANYL}ACETIC ACID
273C1Mod. Amino Acid(2~{S})-2-AZANYL-3-BUTOXY-PROPANOIC ACID
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:438 , ARG A:458 , SER A:460 , GLN A:461 , ARG A:462 , HOH A:703 , HOH A:724 , TYR L:5binding site for residue PO4 A 601
2AC2SOFTWAREARG B:438 , ARG B:458 , SER B:460 , GLN B:461 , ARG B:462 , HOH B:704 , HOH B:721 , TYR M:5binding site for residue PO4 B 601
3AC3SOFTWARESER L:1 , PHE L:2 , ASN L:7 , SER L:8 , PHE L:9 , HOH L:105binding site for Ligand residues 48V L 12 through PRO L 10 bound to SER L 1
4AC4SOFTWAREMET A:495 , ASP A:496 , SER L:1 , PHE L:2 , SER L:8binding site for Ligand 73C L 11 bound to SER L 1
5AC5SOFTWAREMET A:495 , ASP A:496 , SER L:1 , PHE L:2 , SER L:8binding site for Ligand 73C L 11 bound to SER L 8
6AC6SOFTWAREMET B:495 , ASP B:496 , SER M:1 , PHE M:2 , SER M:8binding site for Ligand 73C M 11 bound to SER M 1
7AC7SOFTWAREARG B:427 , THR B:428 , SER M:1 , PHE M:2 , ASN M:7 , SER M:8 , PHE M:9binding site for Ligand residues 48V M 12 through PRO M 10 bound to SER M 1
8AC8SOFTWAREMET B:495 , ASP B:496 , SER M:1 , PHE M:2 , SER M:8binding site for Ligand 73C M 11 bound to SER M 8

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe L:9 -Pro L:10
2Phe M:9 -Pro M:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EEQ)

(-) 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:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeeeeeee..eeeee.........hhhhhhhhhh...........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5eeq A 426 HRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCT 528
                                   435       445       455       465       475       485       495       505       515       525   

Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......hhhhhhhhhhhh.....eeeeee.......eeeeeee..eeeeeeeeeeee..eeeee.........hhhhhhhhhh...........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5eeq B 424 AIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCC 527
                                   433       443       453       463       473       483       493       503       513       523    

Chain L from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5eeq L   1 SFEGYDNSFPxx  12
                                    10||
                                     11-73C
                                      12-48V

Chain M from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5eeq M   1 SFEGYDNSFPxx  12
                                    10||
                                     11-73C
                                      12-48V

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5EEQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRB7_HUMAN | Q144511mw4 1wgr 2l4k 2qms 3pqz 4wwq 4x6s 5d0j 5eel

(-) Related Entries Specified in the PDB File

5eel