PDB entry 1um2

View 1um2 on RCSB PDB site
Description: Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
Class: hydrolase
Keywords: Protein splicing, Vma1-derived endonuclease, VDE, intein, extein, thiazolidine, Hydrolase
Deposited on 2003-09-22, released 2004-09-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-10-09, with a file datestamp of 2019-10-04.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: endonuclease pi-scei
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: VMA1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P17255 (0-453)
      • engineered (0)
      • engineered (78)
    Domains in SCOPe 2.08: d1um2a1, d1um2a2, d1um2a3
  • Chain 'B':
    Compound: endonuclease pi-scei
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: VMA1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P17255 (0-453)
      • engineered (0)
      • engineered (78)
    Domains in SCOPe 2.08: d1um2b1, d1um2b2, d1um2b3
  • Chain 'C':
    Compound: 21-mer from Vacuolar ATP synthase catalytic subunit A
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: VMA1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P17255 (Start-10)
      • engineered (11)
    • Uniprot P17255 (11-End)
  • Chain 'D':
    Compound: 21-mer from Vacuolar ATP synthase catalytic subunit A
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: VMA1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P17255 (Start-10)
      • engineered (11)
    • Uniprot P17255 (11-End)
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1um2A (A:)
sfakgtnvlmadgsiecienievgnkvmgkdgrpreviklprgretmysvvqksqhrahk
sdssrevpellkftcnatnelvvrtprsvrrlsrtikgveyfevitfemgqkkapdgriv
elvkevsksypisegperanelvesyrkasnkayfewtieardlsllgshvrkatyqtya
pilyendhffdymqkskfhltiegpkvlayllglwigdglsdratfsvdsrdtslmervt
eyaeklnlcaeykdrkepqvaktvnlyskvvrgngirnnlntenplwdaivglgflkdgv
knipsflstdnigtretflaglidsdgyvtdehgikatiktihtsvrdglvslarslglv
vsvnaepakvdmngtkhkisyaiymsggdvllnvlskcagskkfrpapaaafarecrgfy
felqelkeddyygitlsddsdhqfllanqvvvhn

    Sequence, based on observed residues (ATOM records): (download) 
    >1um2A (A:)
sfakgtnvlmadgsiecienievgnkvmgkdgrpreviklprgretmysvvqkspellkf
tcnatnelvvrtprsvrrlsrtikgveyfevitfemgqkkapdgrivelvkevsksypis
egperanelvesyrkasnkayfewtieardlsllgshvrkatyqtyapilyendhffdym
qkskfhltiegpkvlayllglwigdglsdratfsvdsrdtslmervteyaeklnlcaeyk
drkepqvaktvnlyskenplwdaivglgflkdgvknipsflstdnigtretflaglidsd
gyvtdehgikatiktihtsvrdglvslarslglvvsvnaepisyaiymsggdvllnvlsk
cagskkfrpapaaafarecrgfyfelqelkeddyygitlsddsdhqfllanqvvvhn

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >1um2B (B:)
sfakgtnvlmadgsiecienievgnkvmgkdgrpreviklprgretmysvvqksqhrahk
sdssrevpellkftcnatnelvvrtprsvrrlsrtikgveyfevitfemgqkkapdgriv
elvkevsksypisegperanelvesyrkasnkayfewtieardlsllgshvrkatyqtya
pilyendhffdymqkskfhltiegpkvlayllglwigdglsdratfsvdsrdtslmervt
eyaeklnlcaeykdrkepqvaktvnlyskvvrgngirnnlntenplwdaivglgflkdgv
knipsflstdnigtretflaglidsdgyvtdehgikatiktihtsvrdglvslarslglv
vsvnaepakvdmngtkhkisyaiymsggdvllnvlskcagskkfrpapaaafarecrgfy
felqelkeddyygitlsddsdhqfllanqvvvhn

    Sequence, based on observed residues (ATOM records): (download) 
    >1um2B (B:)
sfakgtnvlmadgsiecienievgnkvmgkdgrpreviklprgretmysvvqkellkftc
natnelvvrtprsvrrlsrtikgveyfevitfemgqkkapdgrivelvkevsksypiseg
peranelvesyrkasnkayfewtieardlsllgshvrkatyqtyapilyendhffdymqk
skfhltiegpkvlayllglwigdglsdratfsvdsrdtslmervteyaeklnlcaeykdr
kepqvaktvnlyslntenplwdaivglgflkdgvknipsflstdnigtretflaglidsd
gyvtdehgikatiktihtsvrdglvslarslglvvsvnaephkisyaiymsggdvllnvl
skcagskkfrpapaaafarecrgfyfelqelkeddyygitlsddsdhqfllanqvvvhn

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.