5YYD: DNA polymerase IV - ternary complex 15

DNA polymerase IV - ternary complex 15. Determined by X-ray diffraction at 2.05 Å resolution. Released 5 Sept 2018.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Escherichia coli, Escherichia coli K-12
Chains: 6
Atoms: 7,116
Mol. weight: 102.16 kDa
Ligands: TTW
Released: 5 Sept 2018

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

Secondary structure: helices and β-sheets

5YYD contains 35 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: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	8
β-strand	40	1	9
β-strand	41-44	4	8
α-helix	46-49	4
β-strand	58	1	9
α-helix	59-65	7
α-helix	69	1
β-strand	70-72	3	8
α-helix	76-90	15
β-strand	97-101	5	7
β-strand	104-108	5	7
α-helix	115-117	3
α-helix	119-134	16
β-strand	138-143	6	7
α-helix	146-153	8
β-strand	161-163	3	7
α-helix	166-168	3
α-helix	169-174	6
β-strand	177	1	10
α-helix	178-180	3
α-helix	186-193	8
β-strand	199	1	10
α-helix	200-204	5
α-helix	209-215	7
α-helix	217-225	9
α-helix	232-234	3
β-strand	242-253	12	11
α-helix	256-277	22
β-strand	282	1	12
β-strand	285-292	8	11
β-strand	297-303	7	11
β-strand	306	1	12
α-helix	309-323	15
β-strand	329-337	9	11

Chain F: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	12-20	9
α-helix	22-24	3
β-strand	29-32	4	2
β-strand	40	1	3
β-strand	41-44	4	2
α-helix	46-49	4
β-strand	58	1	3
α-helix	59-65	7
β-strand	70-72	3	2
α-helix	76-91	16
β-strand	97-101	5	1
β-strand	104-108	5	1
α-helix	114-117	4
α-helix	119-134	16
β-strand	138-143	6	1
α-helix	146-153	8
β-strand	161-163	3	1
α-helix	169-174	6
β-strand	177	1	4
α-helix	178-180	3
α-helix	186-194	9
β-strand	199	1	4
α-helix	200-204	5
α-helix	208-215	8
α-helix	217-225	9
β-strand	242-253	12	5
α-helix	256-277	22
β-strand	282	1	6
β-strand	285-292	8	5
β-strand	297-303	7	5
β-strand	306	1	6
α-helix	309-321	13
β-strand	329-337	9	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase IV	A, F	protein	352	Escherichia coli	Q47155 (AlphaFold model)
DTN2	B, C, G, H	DNA	18	Escherichia coli K-12

Sequence of entity 1 (A, F), FASTA

>5YYD_1 DNA polymerase IV (chains A, F)
GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPT
GMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSA
TLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLA
KIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERL
RKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLGL

Sequence of entity 2 (B, C, G, H), FASTA

>5YYD_2 DTN2 (chains B, C, G, H)
TCTAGGGTCCTAGGACCC

Ligands and cofactors

ID	Name	Formula	Copies
TTW	5'-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine	C10 H18 N3 O13 P3	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Kottur, J., Nair, D.T. Nucleic Acids Res (2018) 46:5875-5885. DOI 10.1093/nar/gky402 · PubMed

Other PDB entries of the same protein (UniProt Q47155 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
5YUY 1.74 Å, DNA polymerase IV - DNA ternary complex 9
5YUZ 1.83 Å, DNA polymerase IV - DNA ternary complex 11
5YUU 1.89 Å, DNA polymerase IV - DNA ternary complex 4
1UNN 1.9 Å, Complex of beta-clamp processivity factor and little finger domain of PolIV
5YV2 1.9 Å, DNA polymerase IV - DNA ternary complex 14
5YUS 1.94 Å, DNA polymerase IV - DNA ternary complex 2
6IG1 1.97 Å, DNA polymerase IV - DNA ternary complex 10
5YV3 2.03 Å, DNA polymerase IV - DNA ternary complex 7
5YUR 2.04 Å, DNA polymerase IV - DNA ternary complex 1
5YUX 2.04 Å, DNA polymerase IV - DNA ternary complex 8
5YUV 2.06 Å, DNA polymerase IV - DNA ternary complex 5

Browse structure collections

About this viewer

MolViewer shows 5YYD 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.