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(-) Description

Title :  CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH DNMT1(K1115Q)
 
Authors :  Z. M. Zhang, J. Song
Date :  09 Apr 15  (Deposition) - 12 Oct 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Complex, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. M. Zhang, J. Song
Crystal Structure Of Usp7 In Complex With Dnmt1(K1115Q)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 544-1067
    Gene: USP7, HAUSP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- PROCESSING PROTEASE 7
 
Molecule 2 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 1
    Chains: C
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1097-1129
    Gene: DNMT1, AIM, CXXC9, DNMT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE HSAI,M.HSAI,MCMT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:626 , ALA A:636 , MET A:637 , MET A:761 , ASP A:762 , GLN C:1115 , LYS C:1117binding site for residue GOL A 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z97)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:555 -Pro A:556
2Asn A:656 -Pro A:657
3Gly A:848 -Pro A:849
4His A:1072 -Pro A:1073
5Gly C:1110 -Lys C:1111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z97)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z97)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z97)

(-) Sequences/Alignments

Asymmetric/Biological 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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.hhhh...............eeeeee...hhhhhhhhhhhhhh.hhh.eeeeeeee.....eee...........hhhhhhh....eeeeeee...hhhhhh..........eeeeeeeeee....eeeeeeeeeee...hhhhhhhhhhhhhh......eeeeeeee..eeee......hhhhhh......eeeeeee.hhhhhhh...hhhhhhhhhhheeeeeeee........eeeeee...hhhhhhhhhhh....hhh.eeee...................hhhhhh........eeeeeee...hhhhhhh...eeeeee.....eeeeee......hhhhhhhhhhhhh.........eeeeeee..eeeeee...............eeeeee............eeeeeeee......eeeeeeeeee....hhhhhhhhhhhh......eeeeee..eeee.......................eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z97 A  555 GPLGSEAHLYMQVQIVAEDQFCGHQGNDMYDEEKVKYTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFREEEITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIEEIPLDQVDIDENEMLVTVAHFHKEVFGTFGIPFLLRIGEHFREVMKRIQSLLDIQFEKFKFAIVMMGRHQYINEDEYENLKDFEPQPGMSHPRPWLGLDHFN 1083
                                   564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       985       995      1005     |1017      1027   || 1040      1050      1061      1072      1082 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      983|                      1011|             1031|                  1057|     1068|             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       985                       1014              1035                   1059      1070             


Chain C from PDB  Type:PROTEIN  Length:8
                                         
               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
                4z97 C 1110 GKGKGQGK 1117
   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 4Z97)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z97)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z97)

(-) Gene Ontology  (97, 102)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:656 - Pro A:657   [ RasMol ]  
    Gly A:555 - Pro A:556   [ RasMol ]  
    Gly A:848 - Pro A:849   [ RasMol ]  
    Gly C:1110 - Lys C:1111   [ RasMol ]  
    His A:1072 - Pro A:1073   [ RasMol ]  
 

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  4z97
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  UBP7_HUMAN | Q93009
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNMT1_HUMAN | P26358: 3epz 3pta 3swr 4wxx 4yoc 4z96
        UBP7_HUMAN | Q93009: 1nb8 1nbf 1yy6 1yze 2f1w 2f1x 2f1y 2f1z 2foj 2foo 2fop 2kvr 2xxn 2ylm 3mqr 3mqs 4jjq 4kg9 4m5w 4m5x 4pyz 4wph 4wpi 4yoc 4ysi 4z96 5c56 5c6d 5fwi 5gg4 5j7t 5jtj 5jtv

(-) Related Entries Specified in the PDB File

4z96