8PPV

Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) 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	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	B	DP2	polymer	1270	144419.0	1	Pfam (PF03833) UniProt (by SIFTS) (Q9V2F4) In PDB	Pyrococcus abyssi GE5
3	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
4	P	DNA (5'-D(*P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(G7P)P*(PST)P*(PST)P*(PST))-3')	polymer	21	6512.5	1		Pyrococcus abyssi GE5
5	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
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)

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

C, D, E: 1 - 249 (UniProt: Q9UYX8)

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

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

*Water molecules are not included.