2IS6: UvrD-DNA-ADPMgF3 ternary complex

Crystal structure of UvrD-DNA-ADPMgF3 ternary complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 9 Jan 2007.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Escherichia coli
Chains: 4
Atoms: 11,795
Mol. weight: 172.11 kDa
Ligands: ADP, MGF, MG
Released: 9 Jan 2007

Explore 2IS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IS6 contains 85 α-helices and 46 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: 42 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	12-18	7
α-helix	20-21	2
β-strand	25-28	4	1
α-helix	35-48	14
α-helix	54-56	3
β-strand	57-61	5	1
α-helix	64-78	15
β-strand	86-89	4	1
α-helix	90-100	11
β-strand	112-114	3	2
α-helix	116-129	14
α-helix	139-151	13
α-helix	165-184	20
β-strand	186-188	3	2
α-helix	189-202	14
α-helix	204-213	10
β-strand	216-219	4	1
α-helix	222-224	3
α-helix	227-237	11
β-strand	242-247	6	1
α-helix	249-251	3
α-helix	255-257	3
α-helix	262-270	9
β-strand	275-278	4	1
β-strand	281	1	3
α-helix	287-298	12
β-strand	309	1	3
α-helix	317	1
β-strand	318-325	8	4
α-helix	326-342	17
α-helix	347-349	3
β-strand	350-354	5	4
α-helix	357-359	3
α-helix	360-369	10
β-strand	374-376	3	4
α-helix	382-384	3
α-helix	386-399	14
α-helix	404-410	7
α-helix	420-433	14
α-helix	437-445	9
α-helix	452-471	20
α-helix	477-487	11
α-helix	490-495	6
α-helix	500-518	19
α-helix	530-540	11
α-helix	542-544	3
β-strand	554-558	5	4
α-helix	559-562	4
β-strand	567-572	6	4
β-strand	576	1	5
β-strand	578	1	6
β-strand	582	1	6
α-helix	583-586	4
α-helix	592-603	12
β-strand	606-617	12	4
β-strand	618-620	3	7
β-strand	623-625	3	7
α-helix	627-628	2
β-strand	629	1	5
α-helix	630	1
α-helix	631-635	5
α-helix	638-640	3
β-strand	641-643	3	4
α-helix	646-648	3

Chain B: 43 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	12-18	7
β-strand	25-28	4	8
α-helix	35-48	14
α-helix	54-56	3
β-strand	57-61	5	8
α-helix	64-78	15
β-strand	86-89	4	8
α-helix	90-100	11
α-helix	102-105	4
β-strand	112-114	3	9
α-helix	116-129	14
α-helix	139-151	13
α-helix	165-184	20
β-strand	186-188	3	9
α-helix	189-202	14
α-helix	204-213	10
β-strand	216-219	4	8
α-helix	222-224	3
α-helix	227-237	11
β-strand	242-247	6	8
α-helix	249-251	3
α-helix	255-257	3
α-helix	262-270	9
β-strand	275-278	4	8
β-strand	281	1	10
α-helix	287-297	11
β-strand	309	1	10
α-helix	317	1
β-strand	318-323	6	11
α-helix	326-342	17
α-helix	347-349	3
β-strand	350-354	5	11
α-helix	357-359	3
α-helix	360-369	10
β-strand	374-376	3	11
α-helix	382-384	3
α-helix	386-399	14
α-helix	404-410	7
α-helix	420-433	14
α-helix	437-446	10
α-helix	452-471	20
α-helix	477-487	11
α-helix	490-496	7
α-helix	502-517	16
α-helix	530-540	11
α-helix	542-544	3
α-helix	547-548	2
β-strand	554-558	5	11
α-helix	559-562	4
β-strand	567-572	6	11
β-strand	576	1	12
β-strand	578-579	2	13
β-strand	582	1	13
α-helix	583-586	4
α-helix	591-603	13
β-strand	606-615	10	11
β-strand	618-620	3	14
β-strand	623-625	3	14
α-helix	627-628	2
β-strand	629	1	12
α-helix	630	1
α-helix	631-635	5
β-strand	641-643	3	11
α-helix	644-645	2
α-helix	651-653	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(cpgpapgpcpapcptpgpcpapgptpgpcptpcpgptptpgptptpap*t)-3'	C, D	DNA	25
DNA helicase II	A, B	protein	680	Escherichia coli	P03018 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>2IS6_1 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*GP*TP*TP*AP*T)-3' (chains C, D)
CGAGCACTGCAGTGCTCGTTGTTAT

Sequence of entity 2 (A, B), FASTA

>2IS6_2 DNA helicase II (chains A, B)
MDVSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAV
TFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQL
RLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEA
CDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDT
GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENN
NGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQS
RVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIVNRNDDAAFERVVNTPTRGIGD
RTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQ
TDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAAL
EAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSLDEGGRLEEERRLAY
VGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLRATVSRPVSHQRMG
TPMVENDSGYKLGQRVRHAK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MGF	Trifluoromagnesate	F3 Mg	2
MG	Magnesium ion	Mg	2

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

Primary citation

UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Lee, J.Y., Yang, W. Cell (2006) 127:1349-1360. DOI 10.1016/j.cell.2006.10.049 · PubMed

Other PDB entries of the same protein (UniProt P03018 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7EGS 1.7 Å, The crystal structure of lobe domain of E. coli RNA polymerase complexed with the…
3LFU 1.8 Å, Crystal Structure of E. coli UvrD
2IS4 2.6 Å, Crystal structure of UvrD-DNA-ADPNP ternary complex
2IS1 2.9 Å, Crystal structure of UvrD-DNA-SO4 complex
2IS2 3.0 Å, Crystal structure of UvrD-DNA binary complex
6YI2 UvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor…

Browse structure collections

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