PDB entry 6yrw

View 6yrw on RCSB PDB site
Description: SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser
Class: transferase
Keywords: Pyridoxal phosphate; X-ray crystallography; hydroxymethyltransferase; proton abstraction; tetrahydrofolate-independent, transferase
Deposited on 2020-04-20, released 2020-06-03
The last revision prior to the SCOPe 2.07 freeze date was dated 2020-06-03, with a file datestamp of 2020-05-29.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: serine hydroxymethyltransferase
    Species: Streptococcus thermophilus [TaxId:1308]
    Gene: glyA, CDA68_00974, DID82_07515
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5MCK9 (Start-415)
      • engineered mutation (54)
    Domains in SCOPe 2.07: d6yrwa_
  • Chain 'B':
    Compound: serine hydroxymethyltransferase
    Species: Streptococcus thermophilus [TaxId:1308]
    Gene: glyA, CDA68_00974, DID82_07515
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5MCK9 (Start-415)
      • engineered mutation (54)
    Domains in SCOPe 2.07: d6yrwb_
  • Chain 'C':
    Compound: serine hydroxymethyltransferase
    Species: Streptococcus thermophilus [TaxId:1308]
    Gene: glyA, CDA68_00974, DID82_07515
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5MCK9 (Start-415)
      • engineered mutation (54)
    Domains in SCOPe 2.07: d6yrwc_
  • Chain 'D':
    Compound: serine hydroxymethyltransferase
    Species: Streptococcus thermophilus [TaxId:1308]
    Gene: glyA, CDA68_00974, DID82_07515
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5MCK9 (Start-415)
      • engineered mutation (54)
    Domains in SCOPe 2.07: d6yrwd_
  • Heterogens: DSN, GOL, PLP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6yrwA (A:)
mifdkedykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegyp
gkryyggtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmd
lsagghlthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysr
iidfakfreiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggli
ltddediakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadv
fnqhpdfrvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfkts
girvgspaitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

    Sequence, based on observed residues (ATOM records): (download) 
    >6yrwA (A:)
dykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegypgkryyg
gtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmdlsaggh
lthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysriidfak
freiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggliltdded
iakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadvfnqhpd
frvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfktsgirvgs
paitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6yrwB (B:)
mifdkedykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegyp
gkryyggtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmd
lsagghlthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysr
iidfakfreiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggli
ltddediakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadv
fnqhpdfrvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfkts
girvgspaitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

    Sequence, based on observed residues (ATOM records): (download) 
    >6yrwB (B:)
dykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegypgkryyg
gtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmdlsaggh
lthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysriidfak
freiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggliltdded
iakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadvfnqhpd
frvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfktsgirvgs
paitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6yrwC (C:)
mifdkedykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegyp
gkryyggtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmd
lsagghlthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysr
iidfakfreiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggli
ltddediakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadv
fnqhpdfrvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfkts
girvgspaitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

    Sequence, based on observed residues (ATOM records): (download) 
    >6yrwC (C:)
dykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegypgkryyg
gtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmdlsaggh
lthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysriidfak
freiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggliltdded
iakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadvfnqhpd
frvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfktsgirvgs
paitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6yrwD (D:)
mifdkedykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegyp
gkryyggtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmd
lsagghlthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysr
iidfakfreiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggli
ltddediakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadv
fnqhpdfrvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfkts
girvgspaitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply

    Sequence, based on observed residues (ATOM records): (download) 
    >6yrwD (D:)
dykafdpelwnaidaeaerqqnnieliasenvvskavmaaqgtlltnksaegypgkryyg
gtavidvvetlaierakklfgakfanvqphsgsqanaavymsliqpgdtvmgmdlsaggh
lthgapvsfsgktynfvsynvdkeselldydailaqakevrpklivagasaysriidfak
freiadavgaylmvdmahiaglvasghhpspvpyahvttttthktlrgprggliltdded
iakklnsavfpglqggplehviaakavalkealdpafkeygenviknaaamadvfnqhpd
frvisggtnnhlflvdvtkvvengkvaqnvleevnitlnknsipyeqlspfktsgirvgs
paitsrgmgeaesrqiaewmvealenhdkpevlerirgdvkvltdafply