8PPT
Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing a mismatch
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A | DNA polymerase II small subunit | polymer | 662 | 74009.7 | 1 | UniProt (Q9V2F3) Pfam (PF22317) Pfam (PF00149) In PDB | Pyrococcus abyssi GE5 | Pol II,Exodeoxyribonuclease small subunit |
2 | C, D, E | DNA polymerase sliding clamp | polymer | 261 | 29471.8 | 3 | UniProt (Q9UYX8) Pfam (PF00705) Pfam (PF02747) In PDB | Pyrococcus abyssi GE5 | Proliferating cell nuclear antigen homolog,PCNA |
3 | P | DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*GP*CP*TP*TP*T)-3') | polymer | 18 | 5519.5 | 1 | Pyrococcus abyssi GE5 | ||
4 | T | DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3') | polymer | 25 | 7742.0 | 1 | Pyrococcus abyssi GE5 | ||
5 | B | DP2 | polymer | 1270 | 144419.0 | 1 | Pfam (PF03833) UniProt (by SIFTS) (Q9V2F4) In PDB | Pyrococcus abyssi GE5 | |
6 | A, B | MAGNESIUM ION | non-polymer | 24.3 | 3 | Chemie (MG) | |||
7 | B | ZINC ION | non-polymer | 65.4 | 3 | Chemie (ZN) |
Sequence modifications
A: 2 - 619 (UniProt: Q9V2F3)
C, D, E: 1 - 249 (UniProt: Q9UYX8)
PDB | External Database | Details |
---|---|---|
Met -42 | - | initiating methionine |
Gly -41 | - | expression tag |
Lys -40 | - | expression tag |
His -39 | - | expression tag |
His -38 | - | expression tag |
His -37 | - | expression tag |
His -36 | - | expression tag |
Ser -35 | - | expression tag |
Gly -34 | - | expression tag |
His -33 | - | expression tag |
His -32 | - | expression tag |
His -31 | - | expression tag |
Thr -30 | - | expression tag |
Gly -29 | - | expression tag |
His -28 | - | expression tag |
His -27 | - | expression tag |
His -26 | - | expression tag |
His -25 | - | expression tag |
Ser -24 | - | expression tag |
Gly -23 | - | expression tag |
Ser -22 | - | expression tag |
His -21 | - | expression tag |
His -20 | - | expression tag |
His -19 | - | expression tag |
Thr -18 | - | expression tag |
Ser -17 | - | expression tag |
Ser -16 | - | expression tag |
Ser -15 | - | expression tag |
Ala -14 | - | expression tag |
Ser -13 | - | expression tag |
Thr -12 | - | expression tag |
Gly -11 | - | expression tag |
Glu -10 | - | expression tag |
Asn -9 | - | expression tag |
Leu -8 | - | expression tag |
Tyr -7 | - | expression tag |
Phe -6 | - | expression tag |
Gln -5 | - | expression tag |
Gly -4 | - | expression tag |
Thr -3 | - | expression tag |
Gly -2 | - | expression tag |
Asp -1 | - | expression tag |
Gly 0 | - | expression tag |
Ser 1 | - | expression tag |
Ala 451 | His 451 | engineered mutation |
PDB | External Database | Details |
---|---|---|
Met -11 | - | initiating methionine |
Arg -10 | - | expression tag |
Gly -9 | - | expression tag |
Ser -8 | - | expression tag |
His -7 | - | expression tag |
His -6 | - | expression tag |
His -5 | - | expression tag |
His -4 | - | expression tag |
His -3 | - | expression tag |
His -2 | - | expression tag |
Gly -1 | - | expression tag |
Ser 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 7 |
Total formula weight | 320105.5 | |
Non-Polymers* | Number of molecules | 6 |
Total formula weight | 269.1 | |
All* | Total formula weight | 320374.6 |