5BV7: Human LCAT

Crystal structure of human LCAT (L4F, N5D) in complex with Fab of an agonistic antibody. Determined by X-ray diffraction at 2.45 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 5
Atoms: 10,030
Mol. weight: 145.52 kDa
Ligands: NAG
Released: 16 Dec 2015

Explore 5BV7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BV7 contains 53 α-helices and 117 β-strands across 5 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: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	25-28	4	1
β-strand	36-39	4	2
β-strand	41	1	3
β-strand	50	1	4
β-strand	53	1	3
β-strand	58-61	4	2
α-helix	64-67	4
α-helix	71-79	9
β-strand	81-84	4	5
β-strand	89-92	4	5
β-strand	97-99	3	2
α-helix	107-110	4
β-strand	111	1	6
β-strand	119	1	6
α-helix	122-129	8
β-strand	135	1	1
β-strand	139-141	3	1
α-helix	150-152	3
α-helix	154-171	18
α-helix	174	1
β-strand	175-180	6	1
α-helix	182-193	12
α-helix	196-202	7
β-strand	203-209	7	1
α-helix	218-224	7
β-strand	234	1	5
β-strand	246	1	5
α-helix	250-252	3
α-helix	254-255	2
β-strand	264-267	4	7
β-strand	272-274	3	7
α-helix	278-284	7
α-helix	288-297	10
β-strand	311-317	7	1
β-strand	319-326	8	7
α-helix	335-336	2
β-strand	338-345	8	7
β-strand	349	1	7
α-helix	350-353	4
α-helix	354-359	6
β-strand	367-373	7	1
α-helix	377-379	3
α-helix	384-395	12

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	20
β-strand	9-12	4	21
β-strand	17-23	7	20
β-strand	31-37	7	21
β-strand	44-47	4	21
β-strand	48	1	22
β-strand	52	1	22
α-helix	53-54	2
β-strand	61-66	6	20
β-strand	69-75	7	20
β-strand	84-91	8	21
β-strand	94-98	5	21
α-helix	99	1
β-strand	102-106	5	21
α-helix	109-111	3
β-strand	112	1	23
α-helix	113-114	2
β-strand	115-119	5	24
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	24
β-strand	141	1	23
β-strand	146-151	6	25
β-strand	154-156	3	25
β-strand	160-162	3	24
α-helix	163-165	3
β-strand	166-167	2	24
β-strand	173-181	9	24
α-helix	183-187	5
β-strand	192-198	7	25
β-strand	201-207	7	25

Chain C: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	26
β-strand	7	1	27
β-strand	11-12	2	28
β-strand	18-23	6	27
β-strand	24-25	2	26
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	46-51	6	29
β-strand	58-60	3	29
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-99	8	29
β-strand	107	1	4
β-strand	113-116	4	29
β-strand	120-122	3	29
β-strand	123-124	2	28
α-helix	128-129	2
β-strand	130	1	30
α-helix	131-132	2
β-strand	133-137	5	31
β-strand	148-158	11	31
β-strand	159	1	30
β-strand	164-167	4	32
α-helix	168-170	3
β-strand	176-183	8	31
α-helix	184	1
β-strand	189-198	10	31
α-helix	199-201	3
β-strand	208-213	6	32
α-helix	214-216	3
β-strand	218-223	6	32

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-41	8	16
β-strand	47-53	7	16
β-strand	59-61	3	16
α-helix	66-68	3
β-strand	69-74	6	14
β-strand	79-84	6	14
α-helix	89-91	3
β-strand	93-104	12	16
β-strand	109-116	8	16
β-strand	120-122	3	16
β-strand	123-124	2	15
α-helix	128-129	2
β-strand	130	1	17
α-helix	131-132	2
β-strand	133-137	5	18
β-strand	148-158	11	18
β-strand	159	1	17
β-strand	164-167	4	19
β-strand	172	1	19
β-strand	176-178	3	18
α-helix	179-181	3
β-strand	182-183	2	18
β-strand	189-198	10	18
α-helix	199-202	4
β-strand	208-213	6	19
α-helix	214-216	3
β-strand	218-223	6	19

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	9-13	5	9
β-strand	18-23	6	8
α-helix	25-28	4
α-helix	31-32	2
β-strand	33-37	5	9
β-strand	44-47	4	9
β-strand	48	1	10
β-strand	52	1	10
β-strand	61-66	6	8
β-strand	69-74	6	8
α-helix	79-81	3
β-strand	83-90	8	9
β-strand	97-99	3	9
β-strand	103-108	6	9
α-helix	110-112	3
β-strand	113	1	11
α-helix	114-115	2
β-strand	116-120	5	12
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	12
β-strand	142	1	11
β-strand	147-152	6	13
β-strand	155-157	3	13
β-strand	161-163	3	12
α-helix	164-166	3
β-strand	167-168	2	12
β-strand	174-182	9	12
α-helix	184-189	6
β-strand	193-199	7	13
β-strand	202-208	7	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylcholine-sterol acyltransferase	A	protein	422	Homo sapiens	P04180 (AlphaFold model)
27C3 light chain	L	protein	214	Homo sapiens
27C3 heavy chain	H	protein	233	Homo sapiens
Fab1 light chain	B	protein	213	Homo sapiens
Fab1 heavy chain	C	protein	238	Homo sapiens

Sequence of entity 1 (A), FASTA

>5BV7_1 Phosphatidylcholine-sterol acyltransferase (chains A)
FWLFDVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNWMCYRKTEDFFTI
WLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY
LHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYRKLAGLVEEMHAAYGKPVFLIGH
SLGCLHLLYFLLRQPQAWKDRFIDGFISLGAPWGGSIKPMLVLASGDNQGIPIMSSIKLK
EEQRITTTSPWMFPSRMAWPEDHVFISTPSFNYTGRDFQRFFADLHFEEGWYMWLQSRDL
LAGLPAPGVEVYCLYGVGLPTPRTYIYDHGFPYTDPVGVLYEDGDDTVATRSTELCGLWQ
GRQPQPVHLLPLHGIQHLNMVFSNLTLEHINAILLGAYRQGPPASPTASPEPPPPEENLY
FQ

Sequence of entity 2 (L), FASTA

>5BV7_2 27C3 light chain (chains L)
SSELTQDPAVSVALGQTVRITCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDR
FSGSSSGNTASLTITGAQAEDEADYYCNSRDNIGNHQVFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (H), FASTA

>5BV7_3 27C3 heavy chain (chains H)
QVQLQESGPGLVKPSQTLSLTCTVSGASISSGGYNWSWIRQHPGKGLEWIGYIYYSGSTY
YNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARERGYCSSTSCSRVMDVWGQGT
TVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDEVD

Sequence of entity 4 (B), FASTA

>5BV7_4 Fab1 light chain (chains B)
SYELTQPPSVSVSPGQTASITCSGDKLGNKFTSWYQRKPGQSPVLVIYQDTKRPSGIPER
FSGSTSGNTATLTISGTQAMDEADYYCQAWDSSTAWVFGGGTKLEVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (C), FASTA

>5BV7_5 Fab1 heavy chain (chains C)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSNKFY
EDSVKGRFTISRDNSKNTLYLQMDSLRAEDTAVYYCAREGAAVRSFYYSYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSHSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Agonistic Human Antibodies Binding to Lecithin-Cholesterol Acyltransferase Modulate High Density Lipoprotein Metabolism. Gunawardane, R.N., Fordstrom, P., Piper, D.E. et al. J Biol Chem (2016) 291:2799-2811. DOI 10.1074/jbc.M115.672790 · PubMed

Other PDB entries of the same protein (UniProt P04180 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4XWG 2.65 Å, Crystal Structure of LCAT (C31Y) in complex with Fab1
5TXF 3.1 Å, Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in a closed conformation
6MVD 3.1 Å, Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with…
4XX1 3.6 Å, Low resolution structure of LCAT in complex with Fab1
4X96 8.69 Å, Low resolution crystal structure of Lecithin:Cholesterol Acyltransferase (LCAT; residues…
9MXZ 9.8 Å, Lecithin:Cholesterol Acyltransferase Bound to Apolipoprotein A-I dimer in HDL

Browse structure collections

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