3V6O: Leptin Receptor-antibody complex

Leptin Receptor-antibody complex. Determined by X-ray diffraction at 1.95 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 10,514
Mol. weight: 144.46 kDa
Ligands: CYS, NAG
Released: 14 Mar 2012

Explore 3V6O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V6O contains 39 α-helices and 124 β-strands across 6 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	435-438	4	1
β-strand	445-449	5	1
β-strand	462-468	7	2
β-strand	484-486	3	2
β-strand	488-490	3	1
β-strand	496-500	5	1
β-strand	509-515	7	2
β-strand	522-523	2	2
α-helix	524-526	3
β-strand	527-529	3	2
α-helix	531-534	4
β-strand	535	1	1
α-helix	537-540	4
β-strand	544-548	5	3
β-strand	553-557	5	3
β-strand	568-576	9	4
β-strand	584-588	5	4
β-strand	595-598	4	3
β-strand	607-615	9	4
α-helix	622-628	7
β-strand	629-630	2	4
β-strand	632	1	3

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	435-438	4	5
β-strand	445-450	6	5
β-strand	461-468	8	6
β-strand	484-486	3	6
β-strand	489-490	2	5
β-strand	495-500	6	5
β-strand	509-517	9	6
β-strand	520-523	4	6
α-helix	524-526	3
β-strand	527-529	3	6
α-helix	531-534	4
β-strand	535	1	5
α-helix	537-540	4
β-strand	544-548	5	7
β-strand	553-557	5	7
β-strand	568-576	9	8
β-strand	584-587	4	8
β-strand	596-598	3	7
β-strand	607-615	9	8
α-helix	622-628	7
β-strand	629-630	2	8

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
β-strand	13-14	2	10
β-strand	20-27	8	9
β-strand	36-41	6	11
β-strand	48-53	6	11
β-strand	59-61	3	11
α-helix	63-65	3
β-strand	69-74	6	9
α-helix	75-77	3
β-strand	79-84	6	9
α-helix	89-91	3
β-strand	93-101	9	11
β-strand	105-109	5	11
β-strand	113-115	3	11
β-strand	116-117	2	10
α-helix	121-122	2
β-strand	123	1	12
α-helix	124-125	2
β-strand	126-130	5	13
β-strand	138	1	13
β-strand	141-151	11	13
β-strand	152	1	12
β-strand	157-160	4	14
α-helix	161-163	3
β-strand	165	1	14
β-strand	169-171	3	13
α-helix	172-174	3
β-strand	175-176	2	13
β-strand	181-190	10	13
α-helix	191-193	3
β-strand	200-205	6	14
α-helix	206-208	3
β-strand	210-215	6	14

Chain D: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	15
β-strand	13-14	2	16
β-strand	20-27	8	15
β-strand	36-41	6	17
β-strand	48-53	6	17
β-strand	59-61	3	17
α-helix	63-65	3
β-strand	69-74	6	15
β-strand	79-84	6	15
α-helix	89-91	3
β-strand	93-101	9	17
β-strand	105-109	5	17
β-strand	113-115	3	17
β-strand	116-117	2	16
β-strand	123	1	18
α-helix	124-125	2
β-strand	126-130	5	19
β-strand	141-151	11	19
β-strand	152	1	18
β-strand	157-160	4	20
α-helix	161-163	3
β-strand	165	1	20
β-strand	169-171	3	19
α-helix	172-174	3
β-strand	175-177	3	19
β-strand	180-190	11	19
β-strand	200-205	6	20
α-helix	206-208	3
β-strand	210-215	6	20

Chain E: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	21
β-strand	12-16	5	22
β-strand	21-27	7	21
β-strand	35-40	6	22
β-strand	47-51	5	22
β-strand	55-56	2	22
α-helix	57	1
β-strand	64-69	6	21
β-strand	72-77	6	21
α-helix	82-84	3
β-strand	87-92	6	22
α-helix	98	1
β-strand	99-100	2	22
β-strand	104-109	6	22
β-strand	113	1	23
β-strand	116-120	5	24
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	24
β-strand	142	1	23
β-strand	147-152	6	25
β-strand	155-157	3	25
β-strand	161-165	5	24
α-helix	166-169	4
β-strand	175-184	10	24
α-helix	185-189	5
β-strand	193-199	7	25
α-helix	206	1
β-strand	207-212	6	25

Chain F: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	26
β-strand	12-16	5	27
β-strand	21-27	7	26
β-strand	35-40	6	27
β-strand	47-51	5	27
β-strand	55-56	2	27
β-strand	64-69	6	26
β-strand	72-77	6	26
α-helix	82-84	3
β-strand	87-92	6	27
α-helix	98	1
β-strand	99-100	2	27
β-strand	104-109	6	27
β-strand	113	1	28
α-helix	114-115	2
β-strand	116-120	5	29
α-helix	121-123	3
α-helix	124-128	5
β-strand	131-141	11	29
β-strand	142	1	28
β-strand	147-152	6	30
β-strand	155-157	3	30
β-strand	161-165	5	29
α-helix	166-169	4
β-strand	175-184	10	29
α-helix	185-188	4
β-strand	193-199	7	30
α-helix	206	1
β-strand	207-212	6	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leptin receptor	A, B	protein	206	Homo sapiens	P48357 (AlphaFold model)
Monoclonal antibody 9F8 fab fragment Heavy chain	C, D	protein	221	Mus musculus
Monoclonal antibody 9F8 fab fragment Light chain	E, F	protein	215	Mus musculus

Sequence of entity 1 (A, B), FASTA

>3V6O_1 Leptin receptor (chains A, B)
IDVNINISCETDGYLTKMTCRWSTSTIQSLAESTLQLRYHRSSLYCSDIPSIHPISEPKD
CYLQSDGFYECIFQPIFLLSGYTMWIRINHSLGSLDSPPTCVLPDSVVKPLPPSSVKAEI
TINIGLLKISWEKPVFPENNLQFQIRYGLSGKEVQWKMYEVYDAKSKSVSLPVPDLCAVY
AVQVRCKRLDGLGYWSNWSNPAYTVV

Sequence of entity 2 (C, D), FASTA

>3V6O_2 Monoclonal antibody 9F8 fab fragment Heavy chain (chains C, D)
AEVKLLESGPGLVAPSESLSITCTISGFSLTDDGVSWIRQPPGKGLEWLGVIWGGGSTYF
NSLFKSRLSITRDNSKSQVFLEMDSLQTDDTAMYYCAKHDGHETMDYWGQGTSVTVSSSK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCT

Sequence of entity 3 (E, F), FASTA

>3V6O_3 Monoclonal antibody 9F8 fab fragment Light chain (chains E, F)
AEIVMTQSPKFMSTSIGDRVNITCKATQNVRTAVTWYQQKPGQSPQALIFLASNRHTGVP
ARFTGSGSGTDFTLTINNVKSEDLADYFCLQHWNYPLTFGSGTKLEIKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
CYS	Cysteine	C3 H7 N O2 S	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody. Carpenter, B., Hemsworth, G.R., Wu, Z. et al. Structure (2012) 20:487-497. DOI 10.1016/j.str.2012.01.019 · PubMed

Other PDB entries of the same protein (UniProt P48357 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E2P 2.83 Å, Structure of human JAK2 FERM/SH2 in complex with Leptin Receptor
8X85 3.58 Å, Structure of leptin-LepR dimer
7Z3Q 3.62 Å, Crystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution.
8X81 3.77 Å, Structure of leptin-LepR trimer with a large gap
8X80 3.88 Å, Structure of leptin-LepR trimer with a small gap
8AVE 5.62 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…
8AVF 6.45 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…
8AVO 6.84 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…

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