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(-) Description

Title :  SIAH1 BOUND TO SYNTHETIC PEPTIDE (ACE)KLRPVAMVRP(PRK)VR
 
Authors :  E. Santelli, J. L. Stebbins, Y. Feng, S. K. De, A. Purves, K. Motamedchab Z. A. Ronai, R. C. Liddington, M. Pellecchia
Date :  30 Nov 12  (Deposition) - 14 Aug 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sina, Beta Sandwich, Zinc Finger, Ubiquitin Ligase, Covalent Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Stebbins, E. Santelli, Y. Feng, S. K. De, A. Purves, K. Motamedchaboki, B. Wu, Z. A. Ronai, R. C. Liddington, M. Pellecchia
Structure-Based Design Of Covalent Siah Inhibitors.
Chem. Biol. V. 20 973 2013
PubMed-ID: 23891150  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.06.008

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE SIAH1
    Chains: A, C
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 90-282)
    Gene: HUMSIAH, SIAH1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEVEN IN ABSENTIA HOMOLOG 1, SIAH-1, SIAH-1A
 
Molecule 2 - PROTEIN PHYLLOPOD
    Chains: B, D
    Engineered: YES
    Fragment: SIAH-BINDING PEPTIDE (UNP RESIDUES 113-125)
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PRK2Mod. Amino AcidN~6~-PROPANOYL-L-LYSINE
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PRK1Mod. Amino AcidN~6~-PROPANOYL-L-LYSINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3PRK1Mod. Amino AcidN~6~-PROPANOYL-L-LYSINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:97 , LYS B:113BINDING SITE FOR RESIDUE ACE B 112
2AC2SOFTWAREPRO C:97 , LYS D:113BINDING SITE FOR RESIDUE ACE D 112
3AC3SOFTWARECYS A:128 , CYS A:135 , HIS A:147 , HIS A:152BINDING SITE FOR RESIDUE ZN A 601
4AC4SOFTWARECYS A:98 , CYS A:105 , HIS A:117 , CYS A:121BINDING SITE FOR RESIDUE ZN A 602
5AC5SOFTWAREARG A:231 , ARG A:233 , ALA C:222 , ALA C:238 , HOH C:732BINDING SITE FOR RESIDUE MPD A 603
6AC6SOFTWARECYS C:128 , CYS C:135 , HIS C:147 , HIS C:152BINDING SITE FOR RESIDUE ZN C 601
7AC7SOFTWARECYS C:98 , CYS C:105 , HIS C:117 , CYS C:121BINDING SITE FOR RESIDUE ZN C 602
8AC8SOFTWAREALA A:91 , ASN A:92 , SER A:93 , VAL A:94 , LEU A:95 , PHE A:96 , PRO A:97 , THR A:108 , CYS A:130 , LEU A:158 , ASP A:162 , ILE A:163 , VAL A:164 , PHE A:165 , LEU A:166 , THR A:168 , LEU A:172 , VAL A:176 , ASP A:177 , TRP A:178 , VAL A:179 , MET A:180 , GLU A:194 , ARG A:224 , VAL A:277 , THR A:278 , ACE B:112 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204BINDING SITE FOR CHAIN B OF PROTEIN PHYLLOPOD
9AC9SOFTWARESER A:134 , ASN C:92 , SER C:93 , VAL C:94 , LEU C:95 , PHE C:96 , THR C:108 , CYS C:130 , PRO C:131 , THR C:156 , LEU C:158 , GLN C:159 , GLU C:161 , ASP C:162 , ILE C:163 , VAL C:164 , PHE C:165 , LEU C:166 , THR C:168 , PRO C:173 , ALA C:175 , VAL C:176 , ASP C:177 , TRP C:178 , VAL C:179 , GLU C:194 , GLU C:197 , ACE D:112 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:204 , HOH D:205BINDING SITE FOR CHAIN D OF PROTEIN PHYLLOPOD

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I7D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I7D)

(-) Exons   (0, 0)

(no "Exon" information available for 4I7D)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhh...eehhhhhhhhhhhh....ee..........eehhhhhhhhhhhhh...eeee..eeeeee........eeeeeeeee..eeeeeeeeee..eeeeeeee..hhhhhh.eeeeeeeee..eeeeeee..ee....hhhhhhh...eeeehhhhhhhh....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i7d A  91 ANSVLFPCKYASSGCEITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLMHQHKSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEQQFFAIVQLIGTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAENGNLGINVTISMC 282
                                   100       110       120       130       140       150       160       170       180       190      |205       215       225       235       245       255       265       275       
                                                                                                                                    197|                                                                               
                                                                                                                                     203                                                                               


Chain B from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .....eeee..ee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 4i7d B 112 xKLRPVAMVRPkVR 125
                            |      121 |  
                          112-ACE    123-PRK


Chain C from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhh...ee...hhhhhhhhh....ee..........eehhhhhhhhhhhhh....eee..eeeeee........eeeeeeeee..eeeeeeeeeee...eeeeeeeee..hhhhhh.eeeeeeeee..eeeeeee..ee....hhhhhhh...eeeehhhhhhhh....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i7d C  92 NSVLFPCKYASSGCEITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLMHQHKSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEKGHQQFFAIVQLIGTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAENGNLGINVTISMC 282
                                   101       111       121       131       141       151       161       171       181       191      |203       213       223       233       243       253       263       273         
                                                                                                                                    198|                                                                                 
                                                                                                                                     201                                                                                 


Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .....eeee..ee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 4i7d D 112 xKLRPVAMVRPkVR 125
                            |      121 |  
                          112-ACE    123-PRK
   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 4I7D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I7D)

(-) Gene Ontology  (53, 56)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHYL_DROME | Q27934: 4i7b 4i7c
        SIAH1_HUMAN | Q8IUQ4: 2a25 4c9z 4ca1 4i7b 4i7c 4x3g

(-) Related Entries Specified in the PDB File

1k2f 2a25 2an6 4i7b 4i7c