5L2X: Human PrimPol ternary complex

Crystal structure of human PrimPol ternary complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 23 Nov 2016.

Method
X-ray diffraction
Resolution
2.2 Å
Organism
Homo sapiens
Chains
6
Atoms
5,001
Mol. weight
101.35 kDa
Ligands
DTP, CA
Released
23 Nov 2016

Explore 5L2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L2X contains 24 α-helices and 38 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 19 β-strands

ElementResiduesLengthSheet
α-helix2-1615
α-helix36-383
β-strand43-4531
α-helix48-569
β-strand63-6861
α-helix691
β-strand76-8161
α-helix83-908
β-strand99-10241
β-strand10912
β-strand112-11873
α-helix127-14620
α-helix152-1543
β-strand155-15953
β-strand165-17283
β-strand177-17932
α-helix182-19211
α-helix194-1985
α-helix264-2663
β-strand267-26934
β-strand275-27734
β-strand27913
α-helix281-2833
β-strand289-29131
β-strand29315
β-strand29616
β-strand30316
β-strand30415
β-strand305-30623
α-helix314-3163
α-helix322-3309
β-strand342-34432
Chain B: 11 helices, 19 β-strands
ElementResiduesLengthSheet
β-strand42-4547
α-helix48-5811
β-strand63-6867
β-strand76-8167
α-helix83-908
β-strand99-10357
β-strand10912
β-strand112-11878
α-helix127-14620
α-helix152-1543
β-strand155-15958
β-strand165-17288
β-strand177-17932
α-helix182-19716
α-helix264-2663
β-strand267-26939
β-strand275-27739
β-strand27918
α-helix281-2833
β-strand288-29147
α-helix2921
β-strand293110
β-strand296111
β-strand303111
β-strand304110
β-strand305-30628
α-helix314-3163
α-helix322-3309
α-helix335-3373
β-strand342-34432

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed primase/polymerase proteinA, Bprotein353Homo sapiensQ96LW4 (AlphaFold model)
DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')C, GDNA17Homo sapiens
DNA (5'-d(p*gp*gp*tp*ap*gp*cp*(ddg))-3')D, HDNA13Homo sapiens
Sequence of entity 1 (A, B), FASTA
>5L2X_1 DNA-directed primase/polymerase protein (chains A, B)
MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKE
DVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKP
ANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFK
DNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATE
ESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGK
RVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQ
Sequence of entity 2 (C, G), FASTA
>5L2X_2 DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3') (chains C, G)
CATCGCUACCACACCCC
Sequence of entity 3 (D, H), FASTA
>5L2X_3 DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3') (chains D, H)
GGGTGTGGTAGCG

Ligands and cofactors

IDNameFormulaCopies
DTP2'-deoxyadenosine 5'-triphosphateC10 H16 N5 O12 P32
CACalcium ionCa2

Primary citation

Structure and mechanism of human PrimPol, a DNA polymerase with primase activity. Rechkoblit, O., Gupta, Y.K., Malik, R. et al. Sci Adv (2016) 2:e1601317-e1601317. DOI 10.1126/sciadv.1601317 · PubMed

Other PDB entries of the same protein (UniProt Q96LW4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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