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(-) Description

Title :  APLF/XRCC4 COMPLEX
 
Authors :  A. L. Cherry, S. J. Smerdon
Date :  07 Oct 15  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Fha Domain, Aplf, Xrcc4, Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Cherry, T. J. Nott, G. Kelly, S. L. Rulten, K. W. Caldecott, S. J. Smerdon
Versatility In Phospho-Dependent Molecular Recognition Of The Xrcc1 And Xrcc4 Dna-Damage Scaffolds By Aprataxin-Famil Fha Domains.
Dna Repair (Amst. ) V. 35 116 2015
PubMed-ID: 26519825  |  Reference-DOI: 10.1016/J.DNAREP.2015.10.002

(-) Compounds

Molecule 1 - APRATAXIN AND PNK-LIKE FACTOR
    Chains: A, B
    EC Number: 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: APLF, C2ORF13, PALF, XIP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APURINIC-APYRIMIDINIC ENDONUCLEASE APLF,PNK AND APTX-LIKE FHA DOMAIN-CONTAINING PROTEIN,XRCC1-INTERACTING PROTEIN 1
 
Molecule 2 - XRCC4
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SEP2Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:360 , HOH C:403 , HOH C:404 , HOH C:414 , HOH C:415 , HOH C:417binding site for residue MG C 301
2AC2SOFTWAREHOH B:346 , HOH D:401 , HOH D:406 , HOH D:418binding site for residue MG D 301
3AC3SOFTWAREARG B:27 , LYS B:36 , ARG B:40 , HOH B:216 , ALA C:228 , TYR C:229 , ASP C:230 , TPO C:233 , ASP C:234 , HOH C:405 , HOH C:408 , HOH C:412binding site for Di-peptide GLU C 231 and SEP C 232
4AC4SOFTWAREHOH A:301 , ARG B:27 , LYS B:36 , SER B:39 , ARG B:40 , HIS B:58 , ASN B:60 , HOH B:216 , ASP C:230 , GLU C:231 , ASP C:234 , GLU C:235 , HOH C:403 , HOH C:404 , HOH C:405 , HOH C:408 , HOH C:412binding site for residues SEP C 232 and TPO C 233
5AC5SOFTWAREHOH A:301 , ARG B:27 , LYS B:36 , SER B:39 , ARG B:40 , HIS B:58 , ASN B:60 , GLU C:231 , SEP C:232 , GLU C:235 , HOH C:402 , HOH C:403 , HOH C:404 , HOH C:405 , HOH C:407 , HOH C:412binding site for Di-peptide TPO C 233 and ASP C 234
6AC6SOFTWAREARG A:27 , LYS A:36 , ARG A:40 , PRO B:14 , HOH B:216 , HOH B:279 , TYR D:229 , ASP D:230 , TPO D:233 , ASP D:234 , HOH D:403 , HOH D:408binding site for Di-peptide GLU D 231 and SEP D 232
7AC7SOFTWAREARG A:27 , LYS A:36 , SER A:39 , ARG A:40 , HIS A:58 , HOH B:216 , HOH B:274 , GLU D:231 , ASP D:234 , GLU D:235 , HOH D:401 , HOH D:403 , HOH D:404 , HOH D:406 , HOH D:408 , HOH D:409 , HOH D:412binding site for residues SEP D 232 and TPO D 233
8AC8SOFTWAREARG A:27 , LYS A:36 , SER A:39 , ARG A:40 , HIS A:58 , ASN A:60 , HOH B:274 , GLU D:231 , SEP D:232 , GLU D:235 , HOH D:401 , HOH D:403 , HOH D:404 , HOH D:406 , HOH D:409 , HOH D:411 , HOH D:412binding site for Di-peptide TPO D 233 and ASP D 234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E50)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E50)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E50)

(-) Exons   (0, 0)

(no "Exon" information available for 5E50)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......ee...eeeee.................eeeeee..eeeeee......eee.......ee......eee....eeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5e50 A  -4 GPLGSMSGGFELQPRDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAILEVAGGQLRIKPIHTNPCFYQSSEKSQLLPLKPNLWCYLNPGDSFSMLVDKYIFRILSIPSA 106
                                     5        15        25        35        45        55        65        75        85        95       105 


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......ee...eeeee.................eeeeee..eeeeee......eee.......ee......eee....eeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5e50 B  -4 GPLGSMSGGFELQPRDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAILEVAGGQLRIKPIHTNPCFYQSSEKSQLLPLKPNLWCYLNPGDSFSMLVDKYIFRILSIPS 105
                                     5        15        25        35        45        55        65        75        85        95       105


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5e50 C 228 AYDEstDEE 236
                                ||   
                              232-SEP
                               233-TPO


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5e50 D 228 AYDEstDEE 236
                                ||   
                              232-SEP
                               233-TPO
   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 5E50)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E50)

(-) Gene Ontology  (36, 43)

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  5e50
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  APLF_HUMAN | Q8IW19
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  XRCC4_HUMAN | Q13426
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 Related Entries

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

UniProtKB/Swiss-Prot
        APLF_HUMAN | Q8IW19: 2kqb 2kqc 2kqd 2kqe 2kuo
        XRCC4_HUMAN | Q13426: 1fu1 1ik9 3ii6 3mud 3q4f 3rwr 3sr2 3w03 4xa4 5chx 5cj0 5cj4

(-) Related Entries Specified in the PDB File

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