6HMS
Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
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 | 400 | 45078.0 | 1 | UniProt (Q9V2F3) Pfam (PF00149) In PDB | Pyrococcus abyssi | Pol II,Exodeoxyribonuclease small subunit |
2 | B | DNA polymerase II large subunit,DNA polymerase II large subunit | polymer | 1270 | 144419.0 | 1 | UniProt (Q9V2F4) Pfam (PF03833) In PDB | Pyrococcus abyssi | Pol II,Exodeoxyribonuclease large subunit,Pol II,Exodeoxyribonuclease large subunit |
3 | P | DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3') | polymer | 15 | 4636.0 | 1 | Pyrococcus abyssi | ||
4 | T | DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') | polymer | 16 | 4851.1 | 1 | Pyrococcus abyssi | ||
5 | A | FE (III) ION | non-polymer | 55.8 | 1 | Chemie (FE) | |||
6 | A, B | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) |
Sequence modifications
A: 225 - 619 (UniProt: Q9V2F3)
B: 1 - 955 (UniProt: Q9V2F4)
B: 956 - 1270 (UniProt: Q9V2F4)
PDB | External Database | Details |
---|---|---|
Tyr 197 | - | expression tag |
Glu 198 | - | expression tag |
Val 199 | - | expression tag |
Lys 200 | - | expression tag |
Phe 201 | - | expression tag |
Ala 451 | His 451 | conflict |
B: 956 - 1270 (UniProt: Q9V2F4)
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 4 |
Total formula weight | 198984.1 | |
Non-Polymers* | Number of molecules | 5 |
Total formula weight | 317.5 | |
All* | Total formula weight | 199301.6 |