7A1F: Human 5' exonuclease Appollo

Crystal structure of human 5' exonuclease Appollo in complex with 5'dAMP. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Jan 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,905
Mol. weight: 78.87 kDa
Ligands: D5M, NI, FE
Released: 20 Jan 2021

Explore 7A1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A1F contains 37 α-helices and 34 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: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	11-13	3	1
α-helix	18-20	3
β-strand	26-28	3	1
α-helix	34-36	3
β-strand	48-50	3	1
α-helix	52-62	11
α-helix	66-68	3
β-strand	69-71	3	1
β-strand	77-81	5	2
β-strand	89-96	8	2
β-strand	104-110	7	2
β-strand	113-117	5	2
α-helix	125-128	4
α-helix	131-133	3
α-helix	137-139	3
β-strand	141-144	4	2
α-helix	158-170	13
β-strand	176-181	6	3
α-helix	187-196	10
α-helix	200	1
β-strand	201-202	2	3
α-helix	205-211	7
β-strand	220-221	2	3
β-strand	229-233	5	3
α-helix	234-236	3
α-helix	239-245	7
β-strand	251-256	6	3
β-strand	268-271	4	3
α-helix	279-289	11
β-strand	293-296	4	2
α-helix	307-309	3
α-helix	310-313	4
α-helix	315-320	6
α-helix	321-327	7

Chain L: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	4
β-strand	11-13	3	4
α-helix	18-20	3
β-strand	26-28	3	4
α-helix	34-36	3
β-strand	48-50	3	4
α-helix	52-62	11
α-helix	66-68	3
β-strand	69-71	3	4
β-strand	77-81	5	5
β-strand	89-96	8	5
β-strand	104-110	7	5
β-strand	113-117	5	5
α-helix	125-128	4
α-helix	131-133	3
α-helix	137-139	3
β-strand	141-144	4	5
α-helix	158-170	13
β-strand	176-181	6	6
α-helix	187-196	10
α-helix	200	1
β-strand	201-202	2	6
α-helix	205-211	7
β-strand	220-221	2	6
β-strand	229-233	5	6
α-helix	234-236	3
α-helix	239-245	7
β-strand	251-256	6	6
β-strand	268-271	4	6
α-helix	279-289	11
β-strand	293-296	4	5
α-helix	307-309	3
α-helix	310-313	4
α-helix	315-320	6
α-helix	321-327	7
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5' exonuclease Apollo	A, L	protein	342	Homo sapiens	Q9H816 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>7A1F_1 5' exonuclease Apollo (chains A, L)
MNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLHR
HLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFEGYFGTILYTGD
FRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIKIG
LYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEICHS
NMLRWNQTHPTIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSR
RPCGGFQDSLSPRISVPLIPDSVQQYMSSSSRKPSAENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
D5M	2'-deoxyadenosine-5'-monophosphate	C10 H14 N5 O6 P	4
NI	Nickel (II) ion	Ni	2
FE	FE (III) ion	Fe	2

Primary citation

A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family. Baddock, H.T., Newman, J.A., Yosaatmadja, Y. et al. Nucleic Acids Res (2021) 49:9294-9309. DOI 10.1093/nar/gkab692 · PubMed

Other PDB entries of the same protein (UniProt Q9H816 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5AHO 2.16 Å, Crystal structure of human 5' exonuclease Apollo
3BUA 2.5 Å, Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex
7B9B 2.8 Å, Crystal structure of human 5' exonuclease Appollo APO form
7B2X 3.1 Å, Crystal structure of human 5' exonuclease Appollo H61Y variant

Browse structure collections

About this viewer

MolViewer shows 7A1F 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.