8PPU
Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (P) | DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(C7R)P*(PST)P*(PST)P*(PST))-3') | polymer | 21 | 6512.5 | 1 | Pyrococcus abyssi GE5 | ||
| 2 | B (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 | 7717.9 | 1 | Pyrococcus abyssi GE5 | ||
| 3 | C (A) | DNA polymerase II small subunit | polymer | 662 | 74009.7 | 1 | UniProt (Q9V2F3) Pfam (PF22317) Pfam (PF00149) | Pyrococcus abyssi GE5 | |
| 4 | D, E, F (C, D, E) | DNA polymerase sliding clamp | polymer | 261 | 29471.8 | 3 | UniProt (Q9UYX8) Pfam (PF00705) Pfam (PF02747) | Pyrococcus abyssi GE5 | |
| 5 | G (B) | DP2 | polymer | 1270 | 144419.0 | 1 | Pfam (PF03833) UniProt (by SIFTS) (Q9V2F4) | Pyrococcus abyssi GE5 | |
| 6 | H, I, M (A, B) | MAGNESIUM ION | non-polymer | 24.3 | 3 | Chemie (MG) | |||
| 7 | J, K, L (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 | 321074.4 | |
| Non-Polymers* | Number of molecules | 6 |
| Total formula weight | 269.1 | |
| All* | Total formula weight | 321343.5 |
