5DAC: PDB entry 5DAC

ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Chaetomium thermophilum var. thermophilum DSM 1495, synthetic construct
Chains: 4
Atoms: 7,640
Mol. weight: 111.4 kDa
Ligands: MG, AGS, AES
Released: 2 Mar 2016

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

Secondary structure: helices and β-sheets

5DAC contains 32 α-helices and 36 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: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	12	1	2
β-strand	21-24	4	1
β-strand	29-33	5	3
α-helix	40-52	13
α-helix	54-56	3
β-strand	66	1	2
α-helix	69-72	4
β-strand	76-86	11	1
β-strand	92-103	12	1
β-strand	109-113	5	1
β-strand	117-122	6	1
β-strand	125-130	6	1
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
α-helix	159-161	3
α-helix	164-166	3
α-helix	169-179	11
α-helix	183-220	38
α-helix	1102-1159	58
β-strand	1167-1174	8	4
α-helix	1175	1
β-strand	1179-1180	2	5
β-strand	1184-1185	2	5
β-strand	1188-1196	9	4
β-strand	1199-1202	4	4
α-helix	1209-1227	19
β-strand	1232-1237	6	3
α-helix	1245-1262	18
β-strand	1268-1273	6	3
α-helix	1277-1283	7
α-helix	1285-1287	3
β-strand	1291-1297	7	3
β-strand	1303-1309	7	3

Chain B: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
β-strand	12	1	7
β-strand	21-24	4	6
β-strand	29-33	5	8
α-helix	40-52	13
α-helix	54-56	3
β-strand	66	1	7
α-helix	67-68	2
α-helix	69-72	4
β-strand	76-86	11	6
β-strand	92-103	12	6
β-strand	109-113	5	6
β-strand	117-122	6	6
β-strand	125-130	6	6
α-helix	133-144	12
α-helix	148-150	3
α-helix	151-155	5
α-helix	159-161	3
α-helix	164-166	3
α-helix	169-179	11
α-helix	182-220	39
α-helix	1102-1159	58
β-strand	1167-1179	13	9
β-strand	1183-1196	14	9
β-strand	1199-1202	4	9
α-helix	1209-1227	19
β-strand	1232-1237	6	8
α-helix	1245-1263	19
β-strand	1268-1273	6	8
α-helix	1277-1283	7
α-helix	1285-1287	3
β-strand	1291-1297	7	8
β-strand	1303-1309	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putative uncharacterized protein,Putative uncharacterized protein	A, B	protein	449	Chaetomium thermophilum var. thermophilum DSM 1495	G0SHW7 (AlphaFold model)
DNA (5'-d(pcpcpcpcpcpcpcpcpcpcpcpcpcpcp*c)-3')	C	DNA	15	synthetic construct
DNA (5'-d(pgpgpgpgpgpgpgpgpgpgpgpgpgpgp*g)-3')	D	DNA	15	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5DAC_1 Putative uncharacterized protein,Putative uncharacterized protein (chains A, B)
MSKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYATTGELPPNST
RNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQLLVQRNNKRTQKTLEGSLLL
RNNGERTVISTRVAELDKLVSEKLGVPPAILDAVIFCHQDDSLWPMSEPAALKKRFDEIF
EAQKYTKVIENIRLLKKKKGDELKILKEREVQDKANKERAEKVDGGAGGAGGELDLKDAK
AKYKETHIKVETTKAAIEDLGRGMAAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDID
TIQIRSDVESTTSSDSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAES
FCANCGLIALDQPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEFLKYMQCS
DFCDDFYRVKRDEKQNSVIVRESITRITE

Sequence of entity 2 (C), FASTA

>5DAC_2 DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') (chains C)
CCCCCCCCCCCCCCC

Sequence of entity 3 (D), FASTA

>5DAC_3 DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') (chains D)
GGGGGGGGGGGGGGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	2
AES	4-(2-aminoethyl)benzenesulfonyl fluoride	C8 H10 F N O2 S	2

Primary citation

Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50. Seifert, F.U., Lammens, K., Stoehr, G. et al. EMBO J (2016) 35:759-772. DOI 10.15252/embj.201592934 · PubMed

Other PDB entries of the same protein (UniProt G0SHW7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZQY 2.51 Å, Chaetomium thermophilum Rad50 Zn hook
5DA9 3.0 Å, ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding…
7ZR1 4.0 Å, Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)

Browse structure collections

About this viewer

MolViewer shows 5DAC 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.