6TX3: HPF1

HPF1 bound to catalytic fragment of PARP2. Determined by X-ray diffraction at 2.96 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 2.96 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,518
Mol. weight: 68.97 kDa
Ligands: UHB
Released: 19 Feb 2020

Explore 6TX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TX3 contains 28 α-helices and 26 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: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	38-45	8
α-helix	51-63	13
α-helix	68-70	3
α-helix	73-76	4
β-strand	79-80	2	6
α-helix	83-87	5
β-strand	115-120	6	6
β-strand	127-132	6	6
β-strand	142-147	6	6
β-strand	155-156	2	6
α-helix	161-173	13
α-helix	179-199	21
α-helix	208-214	7
β-strand	219	1	7
β-strand	227	1	7
α-helix	245-256	12
α-helix	261-267	7
α-helix	269-283	15
α-helix	288-300	13
α-helix	303-305	3
α-helix	306-319	14
α-helix	323-334	12

Chain B: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	218	1	1
α-helix	223-232	10
β-strand	342	1	1
α-helix	344-349	6
β-strand	354-358	5	2
α-helix	364-375	12
β-strand	384-396	13	2
α-helix	399-402	4
β-strand	410-416	7	2
α-helix	419-421	3
α-helix	422-428	7
α-helix	432	1
α-helix	434	1
β-strand	443	1	3
β-strand	445	1	3
β-strand	448-450	3	4
β-strand	451	1	2
α-helix	454-458	5
α-helix	459-461	3
β-strand	469-478	10	2
β-strand	482-485	4	4
α-helix	494-496	3
β-strand	501-504	4	4
β-strand	508-510	3	5
α-helix	512-514	3
β-strand	516-518	3	2
β-strand	521-523	3	2
β-strand	528-530	3	5
β-strand	543	1	5
β-strand	545-548	4	4
α-helix	551-553	3
β-strand	554-566	13	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2	B	protein	280	Homo sapiens	Q9UGN5 (AlphaFold model)
Histone PARylation factor 1	A	protein	318	Homo sapiens	Q9NWY4 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6TX3_1 Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2 (chains B)
MGSSHHHHHHSSGLVPRGSHPESQLDLRVQELIKLICNVQAMEEKTELQSPEHPLDQHYR
NLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNR
MLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTG
LLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASD
TGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW

Sequence of entity 2 (A), FASTA

>6TX3_2 Histone PARylation factor 1 (chains A)
MGHHHHHHLRKEVENHYKLSLPEDFYHFWKFCEELDPEKPSDSLSASLGLQLVGPYDILA
GKHKTKKKSTGLNFNLHWRFYYDPPEFQTIIIGDNKTQYHMGYFRDSPDEFPVYVGINEA
KKNCIIVPNGDNVFAAVKLFLTKKLKEITDKKKINLLKNIDEKLTEAARELGYSLEQRTV
KMKQRDKKVVTKTFHGAGLVVPVDKNDVGYRELPETDADLKRICKTIVEAASDEERLKAF
APIQEMMTFVQFANDECDYGMGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEI
IEEHLANRSQENIDQLAA

Ligands and cofactors

ID	Name	Formula	Copies
UHB	2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonyl…	C24 H27 N9 O6	1

Primary citation

HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation. Suskiewicz, M.J., Zobel, F., Ogden, T.E.H. et al. Nature (2020) 579:598-602. DOI 10.1038/s41586-020-2013-6 · PubMed

Other PDB entries of the same protein (UniProt Q9UGN5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZZX 1.65 Å, Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor
5D5K 1.9 Å, Crystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB
3KJD 1.95 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
3KCZ 2.0 Å, Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor…
7R59 2.0 Å, PARP2 catalytic domain in complex with OUL245
4TVJ 2.1 Å, Human ARTD2 (PARP2) - catalytic domain in complex with olaparib
8HKO 2.1 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib
9IM8 2.1 Å, Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine…
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
4ZZY 2.2 Å, Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor
6F1K 2.2 Å, Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate
8HLJ 2.24 Å, Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib…

Browse structure collections

About this viewer

MolViewer shows 6TX3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.