5YA1: LsrK-HPr complex with ATP

crystal structure of LsrK-HPr complex with ATP. Determined by X-ray diffraction at 2.7 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Escherichia coli (strain K12)
Chains: 4
Atoms: 8,739
Mol. weight: 138.22 kDa
Ligands: ATP, HEZ, PO4
Released: 11 Jul 2018

Explore 5YA1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YA1 contains 62 α-helices and 52 β-strands across 4 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: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	1
β-strand	24-29	6	1
β-strand	35-41	7	1
α-helix	59-77	19
α-helix	81-83	3
β-strand	84-91	8	1
β-strand	96-99	4	2
α-helix	101-103	3
β-strand	105-109	5	2
α-helix	114-116	3
α-helix	117-129	13
α-helix	131-139	9
α-helix	148-157	10
α-helix	159-162	4
β-strand	167-170	4	2
α-helix	171-180	10
β-strand	185	1	3
α-helix	187-190	4
α-helix	191-193	3
β-strand	196-197	2	4
β-strand	202-203	2	4
α-helix	205-211	7
α-helix	215-218	4
β-strand	221	1	3
β-strand	227-230	4	1
α-helix	233-239	7
α-helix	242	1
β-strand	246-252	7	1
α-helix	253-260	8
β-strand	269-273	5	5
β-strand	277-283	7	5
β-strand	295-298	4	5
β-strand	305-311	7	5
α-helix	315-325	11
α-helix	327-336	10
α-helix	340-350	11
α-helix	352	1
α-helix	355-357	3
β-strand	359-361	3	6
β-strand	377-379	3	6
α-helix	390-416	27
β-strand	423-426	4	5
α-helix	429-431	3
α-helix	433-443	11
β-strand	447-450	4	5
α-helix	456-468	13
α-helix	474-481	8
β-strand	484-488	5	5
α-helix	489-491	3
α-helix	492-501	10

Chain B: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	7
β-strand	23-29	7	7
β-strand	35-42	8	7
α-helix	59-77	19
α-helix	81-83	3
β-strand	84-91	8	7
β-strand	96-99	4	8
α-helix	101-103	3
β-strand	105-109	5	8
α-helix	114-116	3
α-helix	117-129	13
α-helix	131-139	9
α-helix	148-157	10
α-helix	159-162	4
β-strand	167-170	4	8
α-helix	171-180	10
β-strand	185	1	9
α-helix	187-190	4
α-helix	191-193	3
β-strand	196-197	2	10
β-strand	202-203	2	10
α-helix	205-211	7
α-helix	215-218	4
β-strand	221	1	9
β-strand	227-230	4	7
α-helix	233-239	7
α-helix	242	1
β-strand	246-252	7	7
α-helix	253-260	8
β-strand	269-273	5	11
β-strand	277-283	7	11
β-strand	295-298	4	11
β-strand	305-311	7	11
α-helix	315-325	11
α-helix	327-336	10
α-helix	340-350	11
α-helix	352	1
α-helix	355-357	3
β-strand	359-361	3	12
β-strand	377-379	3	12
α-helix	390-416	27
β-strand	423-426	4	11
α-helix	429-431	3
α-helix	433-443	11
β-strand	447-450	4	11
α-helix	456-468	13
α-helix	474-481	8
β-strand	484-488	5	11
α-helix	489-491	3
α-helix	492-499	8

Chains C and D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	13
α-helix	16-26	11
β-strand	32-37	6	13
β-strand	40-43	4	13
α-helix	47-51	5
β-strand	60-66	7	13
α-helix	70-83	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autoinducer-2 kinase	A, B	protein	540	Escherichia coli (strain K12)	P77432 (AlphaFold model)
Phosphocarrier protein HPr	C, D	protein	85	Escherichia coli (strain K12)	P0AA04 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5YA1_1 Autoinducer-2 kinase (chains A, B)
HHHHHHSEDPMARLFTLSESKYYLMALDAGTGSIRAVIFDLEGNQIAVGQAEWRHLAVPD
VPGSMEFDLNKNWQLACECMRQALHNAGIAPEYIAAVSACSMREGIVLYNNEGAPIWACA
NVDARAAREVSELKELHNNTFENEVYRATGQTLALSAIPRLLWLAHHRSDIYRQASTITM
ISDWLAYMLSGELAVDPSNAGTTGLLDLTTRDWKPALLDMAGLRADILSPVKETGTLLGV
VSSQAAELCGLKAGTPVVVGGGDVQLGCLGLGVVRPAQTAVLGGTFWQQVVNLAAPVTDP
EMNVRVNPHVIPGMVQAESISFFTGLTMRWFRDAFCAEEKLIAERLGIDTYTLLEEMASR
VPPGSWGVMPIFSDRMRFKTWYHAAPSFINLSIDPDKCNKATLFRALEENAAIVSACNLQ
QIADFSNIHPSSLVFAGGGSKGKLWSQILADVSGLPVNIPVVKEATALGCAIAAGVGAGI
FSSMAETGERLVRWERTHTPDPEKHELYQDSRDKWQAVYQDQLGLVDHGLTTSLWKAPGL

Sequence of entity 2 (C, D), FASTA

>5YA1_2 Phosphocarrier protein HPr (chains C, D)
MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTV
VTISAEGEDEQKAVEHLVKLMAELE

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
HEZ	Hexane-1,6-diol	C6 H14 O2	4
PO4	Phosphate ion	O4 P	8

Primary citation

Evidence of link between quorum sensing and sugar metabolism inEscherichia colirevealed via cocrystal structures of LsrK and HPr. Ha, J.H., Hauk, P., Cho, K. et al. Sci Adv (2018) 4:eaar7063-eaar7063. DOI 10.1126/sciadv.aar7063 · PubMed

Other PDB entries of the same protein (UniProt P77432 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YA2 2.7 Å, Crystal structure of LsrK-HPr complex with ADP
5YA0 3.0 Å, Crystal structure of LsrK and HPr complex

Browse structure collections

About this viewer

MolViewer shows 5YA1 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.