5K59: LukGH from Staphylococcus aureus

Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody. Determined by X-ray diffraction at 2.84 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 2.84 Å
Organisms: Staphylococcus aureus (strain USA300), Homo sapiens
Chains: 8
Atoms: 15,764
Mol. weight: 241.27 kDa
Ligands: PO4
Released: 10 Aug 2016

Explore 5K59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K59 contains 42 α-helices and 180 β-strands across 8 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: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	18
β-strand	19-29	11	18
β-strand	34-44	11	18
β-strand	48	1	13
β-strand	50-62	13	18
β-strand	66-67	2	19
β-strand	75-90	16	19
β-strand	97-103	7	18
β-strand	112-119	8	20
β-strand	123-126	4	13
β-strand	133	1	13
α-helix	135-137	3
β-strand	142-149	8	20
β-strand	153-157	5	19
β-strand	165-172	8	19
β-strand	175-177	3	21
β-strand	180-182	3	21
β-strand	195	1	19
β-strand	200	1	22
α-helix	209-211	3
β-strand	213	1	22
α-helix	216-218	3
α-helix	221-224	4
β-strand	226-227	2	18
β-strand	231-238	8	18
β-strand	244-264	21	19
β-strand	269-291	23	19
β-strand	296-303	8	19

Chain B: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	7
β-strand	19-29	11	7
β-strand	34-44	11	7
β-strand	48	1	1
β-strand	50-62	13	7
β-strand	66-67	2	8
β-strand	75-90	16	8
β-strand	97-103	7	7
β-strand	112-119	8	9
β-strand	123-125	3	1
β-strand	126-127	2	10
β-strand	132-133	2	10
α-helix	135-137	3
β-strand	142-149	8	9
β-strand	153-157	5	8
β-strand	165-172	8	8
β-strand	175-177	3	11
β-strand	180-182	3	11
β-strand	195	1	8
β-strand	200	1	12
α-helix	209-211	3
β-strand	213	1	12
α-helix	216-218	3
α-helix	221-224	4
β-strand	226-227	2	7
β-strand	231-238	8	7
β-strand	244-264	21	8
β-strand	269-291	23	8
β-strand	296-303	8	8

Chain C: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	43-55	13	13
β-strand	60-70	11	13
β-strand	76-88	13	13
β-strand	92-95	4	14
β-strand	103-118	16	14
β-strand	123-129	7	13
β-strand	133-134	2	14
β-strand	138-145	8	15
β-strand	151-154	4	15
β-strand	165-172	8	15
β-strand	176-180	5	14
β-strand	188-195	8	14
β-strand	197-200	4	16
β-strand	203-206	4	16
β-strand	214	1	17
α-helix	225-228	4
β-strand	229	1	17
α-helix	232-234	3
α-helix	237-240	4
β-strand	242-243	2	13
β-strand	247-254	8	13
β-strand	259-275	17	14
β-strand	285-302	18	14
β-strand	307-316	10	14

Chain D: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	44-55	12	1
β-strand	60-70	11	1
β-strand	76-88	13	1
β-strand	92-95	4	2
β-strand	103-118	16	2
β-strand	123-129	7	1
β-strand	133-134	2	2
β-strand	138-145	8	3
β-strand	151-154	4	3
β-strand	165-172	8	3
β-strand	176-180	5	2
β-strand	188-195	8	2
β-strand	197-200	4	4
β-strand	203-206	4	4
β-strand	214	1	5
β-strand	221	1	6
β-strand	224	1	6
α-helix	225-228	4
β-strand	229	1	5
α-helix	232-234	3
α-helix	237-240	4
β-strand	242-243	2	1
β-strand	247-254	8	1
β-strand	259-275	17	2
β-strand	285-302	18	2
β-strand	307-316	10	2

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	33
β-strand	11-12	2	34
β-strand	18-25	8	33
β-strand	35-41	7	35
β-strand	48-53	6	35
β-strand	59-61	3	35
α-helix	66-68	3
β-strand	69-74	6	33
β-strand	79-84	6	33
α-helix	89-91	3
β-strand	93-100	8	35
β-strand	106-109	4	35
β-strand	113-115	3	35
β-strand	116-117	2	34
α-helix	120-122	3
β-strand	123	1	36
α-helix	124-125	2
β-strand	126-130	5	37
β-strand	140-150	11	37
β-strand	151	1	36
β-strand	156-159	4	38
α-helix	160-162	3
β-strand	168-170	3	37
α-helix	171-173	3
β-strand	174-175	2	37
β-strand	181-190	10	37
α-helix	192-194	3
β-strand	201-205	5	38
β-strand	210-214	5	38

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	39
β-strand	10-14	5	35
β-strand	19-25	7	39
β-strand	33-38	6	35
β-strand	45-49	5	35
β-strand	53-54	2	35
α-helix	55	1
β-strand	62-67	6	39
β-strand	70-75	6	39
α-helix	80-82	3
β-strand	84-90	7	35
α-helix	96	1
β-strand	97-98	2	35
β-strand	102-107	6	35
β-strand	111	1	40
β-strand	114-118	5	41
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	41
β-strand	140	1	40
β-strand	144-150	7	42
β-strand	154	1	42
β-strand	159-163	5	41
α-helix	164-167	4
β-strand	173-182	10	41
α-helix	183-188	6
β-strand	191-198	8	42
β-strand	205-210	6	42

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	11-12	2	24
β-strand	18-25	8	23
β-strand	34-41	8	25
β-strand	48-54	7	25
β-strand	59-61	3	25
α-helix	66-68	3
β-strand	69-74	6	23
β-strand	79-84	6	23
α-helix	89-91	3
β-strand	93-101	9	25
β-strand	106-109	4	25
β-strand	113-115	3	25
β-strand	116-117	2	24
α-helix	120-122	3
β-strand	123	1	26
α-helix	124-125	2
β-strand	126-130	5	27
β-strand	140-150	11	27
β-strand	151	1	26
β-strand	156-159	4	28
α-helix	160-162	3
β-strand	168-170	3	27
α-helix	171-173	3
β-strand	174-175	2	27
β-strand	181-190	10	27
α-helix	192-194	3
β-strand	200-205	6	28
β-strand	210-215	6	28

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	29
β-strand	10-14	5	25
β-strand	19-25	7	29
β-strand	33-38	6	25
β-strand	45-49	5	25
β-strand	53-54	2	25
α-helix	55	1
β-strand	62-67	6	29
β-strand	70-75	6	29
α-helix	80-82	3
β-strand	84-90	7	25
α-helix	96	1
β-strand	97-98	2	25
β-strand	99	1	29
β-strand	102-107	6	25
β-strand	111	1	30
β-strand	114-118	5	31
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	31
β-strand	140	1	30
β-strand	144-150	7	32
β-strand	154	1	32
β-strand	159-163	5	31
α-helix	164-167	4
β-strand	173-182	10	31
α-helix	183-188	6
β-strand	191-198	8	32
β-strand	205-210	6	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized leukocidin-like protein 2	C, D	protein	319	Staphylococcus aureus (strain USA300)	Q2FWP0 (AlphaFold model)
Uncharacterized leukocidin-like protein 1	A, B	protein	311	Staphylococcus aureus (strain USA300)	Q2FFA3 (AlphaFold model)
Fab heavy chain	E, H	protein	227	Homo sapiens
Fab light chain	F, L	protein	214	Homo sapiens

Sequence of entity 1 (C, D), FASTA

>5K59_1 Uncharacterized leukocidin-like protein 2 (chains C, D)
DSQDQNKKEHVDKSQQKDKRNVTNKDKNSTAPDDIGKNGKITKRTETVYDEKTNILQNLQ
FDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYHVDFQVKRNRKTEI
LDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYNQQNYDTIASGKNN
NWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASKYRYPALVRSGFNP
EFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDGQRLIVTYEVDWKN
KTVKVVDKYSDDNKPYKEG

Sequence of entity 2 (A, B), FASTA

>5K59_2 Uncharacterized leukocidin-like protein 1 (chains A, B)
SLKINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAK
GTIGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYG
YKTGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNM
GHDHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHD
KKDKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVK
FVKVLNDNEKK

Sequence of entity 3 (E, H), FASTA

>5K59_3 Fab heavy chain (chains E, H)
ELQLQESGPGLVKPSETLSLTCTVSGGSISSGSYYWDWIRQPPGKGLEWIGNIYKSGSTY
YNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARERGMHYMDVWGKGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 4 (F, L), FASTA

>5K59_4 Fab light chain (chains F, L)
DIQMTQSPSSLSASVGDRVTITCRASQSINSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQQFDPPFTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (PG4, CL) are not listed.

Primary citation

Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. Badarau, A., Rouha, H., Malafa, S. et al. MAbs (2016) 8:1347-1360. DOI 10.1080/19420862.2016.1215791 · PubMed

Other PDB entries of the same protein (UniProt Q2FWP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RHV 2.29 Å, Crystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus…
6RHW 2.75 Å, Crystal structure of human CD11b I-domain (CD11b-I) in complex with Staphylococcus…
7T87 3.0 Å, Crystal structure of leukocidin ab/centyrin S17/FAB 214F complex

Browse structure collections

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