PDB entry 6vdd

View 6vdd on RCSB PDB site
Description: pol domain of pol1 from m. smegmatis complex with dna primer-template and dntp
Deposited on 2019-12-24, released 2020-02-12
The last revision was dated 2020-04-15, with a file datestamp of 2020-04-10.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: N/A
AEROSPACI score: 0.34 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase I
    Species: Mycolicibacterium smegmatis [TaxId:1772]
    Gene: polA, MSMEI_3749
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA (5'-d(*gp*cp*gp*ap*tp*cp*ap*cp*gp*tp*a*(dct))-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'C':
    Compound: DNA (5'-d(p*cp*gp*tp*ap*cp*gp*tp*gp*ap*tp*cp*gp*cp*a)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'D':
    Compound: DNA polymerase I
    Species: Mycolicibacterium smegmatis [TaxId:1772]
    Gene: polA, MSMEI_3749
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA (5'-d(*gp*cp*gp*ap*tp*cp*ap*cp*gp*tp*a*(dct))-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'F':
    Compound: DNA (5'-d(p*gp*tp*ap*cp*gp*tp*gp*ap*tp*cp*gp*cp*a)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Heterogens: MG, DCT, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6vddA (A:)
fetlvavepevehgfdvrgralepgelaawlsehslgsrfgvavvgthkaydadatalai
vaadgdgryidtstltpedeaalaswladpgppkalheaklamhdlagrgwtlrgvtsdt
alaaylvrpgqrsftlddlavrylhrelraetpeqqqlsllddsdgvdeqavqtvilrac
avldladaldqelaridslsllsrmelpvqrtlaemehagiavdlgmleqlqsefadqir
daaeaaysvigkqinlgspkqlqavlfdelempktkktktgyttdadalqslfektghpf
lqhllahrdatrlkvtvdgllnsvasdgrihttfnqtiaatgrlsstepnlqnipirtea
grrirdafvvgegyaelmtadysqiemrimahlsrdaglieafntgedlhsfvasrafsv
pidevtpelrrrvkamsyglayglsayglaqqlkisteeakvqmeqyfdrfggvrdylrd
vvdqarkdgytstvlgrrrylpeldssnrqvreaaeraalnapiqgsaadiikvaminvd
qaikdaglrsrillqvhdellfevsegeqgeleqlvrehmgnaypldvplevsvgygrsw
daaah

    Sequence, based on observed residues (ATOM records):
    >6vddA (A:)
rgralepgelaawlsehslgsrfgvavvgthkaydadatalaivaadgdgryidtstltp
edeaalaswladpgppkalheaklamhdlagrgwtlrgvtsdtalaaylvrpgqrsftld
dlavrylhrelravqtvilracavldladaldqelaridslsllsrmelpvqrtlaemeh
agiavdlgmleqlqsefadqirdaaeaaysvigkqinlgspkqlqavlfdelempktkkt
ktgyttdadalqslfektghpflqhllahrdatrlkvtvdgllnsvasdgrihttfnqti
aatgrlsstepnlqnipirteagrrirdafvvgegyaelmtadysqiemrimahlsrdag
lieafntgedlhsfvasrafsvpidevtpelrrrvkamsyglayglsayglaqqlkiste
eakvqmeqyfdrfggvrdylrdvvdqarkdgytstvlgrrrylpeldssnrqvreaaera
alnapiqgsaadiikvaminvdqaikdaglrsrillqvhdellfevsegeqgeleqlvre
hmgnaypldvplevsvgygrswdaaah

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6vddD (D:)
fetlvavepevehgfdvrgralepgelaawlsehslgsrfgvavvgthkaydadatalai
vaadgdgryidtstltpedeaalaswladpgppkalheaklamhdlagrgwtlrgvtsdt
alaaylvrpgqrsftlddlavrylhrelraetpeqqqlsllddsdgvdeqavqtvilrac
avldladaldqelaridslsllsrmelpvqrtlaemehagiavdlgmleqlqsefadqir
daaeaaysvigkqinlgspkqlqavlfdelempktkktktgyttdadalqslfektghpf
lqhllahrdatrlkvtvdgllnsvasdgrihttfnqtiaatgrlsstepnlqnipirtea
grrirdafvvgegyaelmtadysqiemrimahlsrdaglieafntgedlhsfvasrafsv
pidevtpelrrrvkamsyglayglsayglaqqlkisteeakvqmeqyfdrfggvrdylrd
vvdqarkdgytstvlgrrrylpeldssnrqvreaaeraalnapiqgsaadiikvaminvd
qaikdaglrsrillqvhdellfevsegeqgeleqlvrehmgnaypldvplevsvgygrsw
daaah

    Sequence, based on observed residues (ATOM records):
    >6vddD (D:)
gralepgelaawlsehslgsrfgvavvgthkaydadatalaivaadgdgryidtstltpe
deaalaswladpgppkalheaklamhdlagrgwtlrgvtsdtalaaylvrpgqrsftldd
lavrylhrelrqavqtvilracavldladaldqelaridslsllsrmelpvqrtlaemeh
agiavdlgmleqlqsefadqirdaaeaaysvigkqinlgspkqlqavlfdelempktkkt
ktgyttdadalqslfektghpflqhllahrdatrlkvtvdgllnsvasdgrihttfnqti
aatgrlsstepnlqnipirteagrrirdafvvgegyaelmtadysqiemrimahlsrdag
lieafntgedlhsfvasrafsvpidevtpelrrrvkamsyglayglsayglaqqlkiste
eakvqmeqyfdrfggvrdylrdvvdqarkdgytstvlgrrrylpeldssnrqvreaaera
alnapiqgsaadiikvaminvdqaikdaglrsrillqvhdellfevsegeqgeleqlvre
hmgnaypldvplevsvgygrswdaaah

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.