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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH THE DESIGNED HIGH-AFFINITY PEPTIDE LIGAND P7 AT PH 8
 
Authors :  A. Camara-Artigas
Date :  16 Feb 13  (Deposition) - 29 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  B,H  (1x)
Biol. Unit 3:  C,L  (1x)
Biol. Unit 4:  D,K  (1x)
Biol. Unit 5:  E,J  (1x)
Biol. Unit 6:  F,I  (1x)
Keywords :  Beta Shandwich, Sh3 Domain, Kinase, Poly Proline Rich Motifs, Transferase, Transferase-Unknown Function Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Camara-Artigas
Crystal Structure Of The Abl-Sh3 Domain Complexed With The Designed High-Affinity Peptide Ligand P7
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ABL1
    Chains: A, B, C, D, E, F
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: SH3 DOMAIN
    Gene: ABL, ABL1, JTK7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: PBAT4
    Synonym: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1, ABELSON TYROSINE-PROTEIN KINASE 1, PROTO-ONCOGENE C-ABL, P150
 
Molecule 2 - P7
    Chains: G, H, I, J, K, L
    Engineered: YES
    Other Details: THIS SEQUENCE HAS BEEN OPTIMIZED TO INCREASE THE AFFINITY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A     G     
Biological Unit 2 (1x):  B     H    
Biological Unit 3 (1x):   C        L
Biological Unit 4 (1x):    D      K 
Biological Unit 5 (1x):     E    J  
Biological Unit 6 (1x):      F  I   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:243 , GLU E:86 , LYS E:87 , LYS E:105 , HOH E:338BINDING SITE FOR RESIDUE SO4 E 201
2AC2SOFTWARETYR A:70 , SER A:75 , ASP A:77 , THR A:79 , ASN A:94 , GLU A:98 , TRP A:99 , ASN A:106 , TRP A:110 , ASN A:114 , TYR A:115 , HOH A:221 , HOH A:241 , HOH A:263 , LYS B:84 , HOH B:229 , PRO D:118 , HOH G:102 , HOH G:103 , HOH G:104 , HOH G:105 , HOH G:106 , HOH G:108 , HOH G:109 , HOH G:110 , PRO H:10BINDING SITE FOR CHAIN G OF P7
3AC3SOFTWARETYR A:70 , HOH A:219 , TYR B:70 , SER B:75 , ASN B:78 , THR B:79 , ASN B:94 , GLU B:98 , TRP B:99 , LYS B:105 , TRP B:110 , ASN B:114 , TYR B:115 , HOH B:213 , HOH B:220 , PRO G:10 , HOH H:101 , HOH H:102 , HOH H:103 , HOH H:104 , HOH H:105 , HOH H:107 , HOH H:112 , HOH H:113 , HOH H:116 , HOH H:117 , HOH H:118BINDING SITE FOR CHAIN H OF P7
4AC4SOFTWAREHOH E:301 , HOH E:316 , TYR F:70 , SER F:75 , ASN F:78 , THR F:79 , ASN F:94 , GLU F:98 , TRP F:99 , LYS F:105 , ASN F:106 , TRP F:110 , TYR F:115 , HOH F:203 , HOH F:207 , HOH F:251 , HOH I:101 , HOH I:102 , HOH I:103 , HOH I:104 , HOH I:106 , HOH I:108 , HOH I:109 , HOH I:110BINDING SITE FOR CHAIN I OF P7
5AC5SOFTWARETHR C:117 , PRO C:118 , HOH C:220 , SER E:75 , ASP E:77 , THR E:79 , ASN E:94 , GLU E:98 , TRP E:99 , ASN E:106 , TRP E:110 , ASN E:114 , TYR E:115 , HOH E:302 , HOH E:315 , HOH E:324 , HOH E:335 , HOH E:355 , TYR F:70 , LYS F:84 , HOH J:101 , HOH J:103 , HOH J:104 , HOH J:105 , HOH J:107 , HOH J:109BINDING SITE FOR CHAIN J OF P7
6AC6SOFTWARETYR D:70 , SER D:75 , ASP D:77 , ASN D:78 , THR D:79 , ASN D:94 , GLU D:98 , TRP D:99 , ASN D:106 , TRP D:110 , ASN D:114 , TYR D:115 , HOH D:207 , HOH D:254 , HOH K:101 , HOH K:102 , HOH K:103 , HOH K:104 , HOH K:106 , HOH K:109BINDING SITE FOR CHAIN K OF P7
7AC7SOFTWARETYR C:70 , SER C:75 , GLY C:76 , ASP C:77 , ASN C:78 , THR C:79 , ASN C:94 , GLU C:98 , TRP C:99 , LYS C:105 , ASN C:106 , TRP C:110 , ASN C:114 , TYR C:115 , HOH C:205 , HOH C:216 , HOH D:232 , HOH L:101 , HOH L:102 , HOH L:103BINDING SITE FOR CHAIN L OF P7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J9H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:62 -Pro A:63
2Pro G:9 -Pro G:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J9H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J9H)

(-) Exons   (0, 0)

(no "Exon" information available for 4J9H)

(-) 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:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeeee.....eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 4j9h A  62 DPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVN 120
                                    71        81        91       101       111         


Chain B from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4j9h B  64 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV 119
                                    73        83        93       103       113      


Chain C from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4j9h C  64 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV 119
                                    73        83        93       103       113      


Chain D from PDB  Type:PROTEIN  Length:57
                                                                                         
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeeee.....eeeeee..eeeeee...eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 4j9h D  64 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVN 120
                                    73        83        93       103       113       


Chain E from PDB  Type:PROTEIN  Length:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeeeee....eeeeee..eeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 4j9h E  62 DPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVN 120
                                    71        81        91       101       111         


Chain F from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..................eeeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 4j9h F  64 NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV 119
                                    73        83        93       103       113      


Chain G from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h G   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE      


Chain H from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h H   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE      


Chain I from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h I   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE      


Chain J from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h J   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE      


Chain K from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h K   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE      


Chain L from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4j9h L   0 xAPTYPPPPPP  10
                            |        9 
                            0-ACE
   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 4J9H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J9H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J9H)

(-) Gene Ontology  (125, 125)

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  4j9h
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  2.7.10.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ABL1_HUMAN | P00519: 1ab2 1abl 1awo 1bbz 1ju5 1opl 1zzp 2abl 2e2b 2f4j 2fo0 2g1t 2g2f 2g2h 2g2i 2gqg 2hiw 2hyy 2hz0 2hz4 2hzi 2o88 2v7a 3cs9 3eg0 3eg1 3eg2 3eg3 3egu 3k2m 3pyy 3qri 3qrj 3qrk 3t04 3ue4 3uyo 4j9b 4j9c 4j9d 4j9e 4j9f 4j9g 4j9i 4jjb 4jjc 4jjd 4twp 4wa9 4xey 4yc8 4zog 5dc0 5dc4 5dc9 5hu9 5mo4 5oaz

(-) Related Entries Specified in the PDB File

2o88 CRYSTAL STRUCTURE OF THE N114A MUTANT OF ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS
3eg0 CRYSTAL STRUCTURE OF THE N114T MUTANT OF ABL-SH3 DOMAIN
3eg1 CRYSTAL STRUCTURE OF THE N114Q MUTANT OF ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS
3eg2 CRYSTAL STRUCTURE OF THE N114Q MUTANT OF ABL-SH3 DOMAIN
3eg3 CRYSTAL STRUCTURE OF THE N114A MUTANT OF ABL-SH3 DOMAIN
3egu CRYSTAL STRUCTURE OF THE N114A MUTANT OF ABL-SH3 DOMAIN
4j9f
4j9g
4j9i