6KO5: Complex structure of Ghrelin receptor with Fab

Complex structure of Ghrelin receptor with Fab. Determined by X-ray diffraction at 3.3 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Escherichia coli, Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,543
Mol. weight: 95.99 kDa
Ligands: 8QX
Released: 12 Aug 2020

Explore 6KO5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KO5 contains 28 α-helices and 47 β-strands across 3 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: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1018	16
α-helix	1023-1042	20
α-helix	1044-1045	2
α-helix	1046-1048	3
α-helix	1056-1081	26
α-helix	1084-1104	21
α-helix	40-69	30
α-helix	72-74	3
α-helix	77-104	28
α-helix	113-146	34
α-helix	150-153	4
α-helix	157-174	18
α-helix	178-181	4
β-strand	182-185	4	1
α-helix	192-195	4
β-strand	197-200	4	1
α-helix	203-206	4
α-helix	209-239	31
α-helix	255-289	35
α-helix	302-326	25
α-helix	328-338	11

Chain H: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	10-12	3	3
β-strand	18-25	8	2
β-strand	33-40	8	3
β-strand	44-51	8	3
β-strand	58-60	3	3
β-strand	65	1	2
β-strand	68-73	6	2
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	106-108	3	3
β-strand	112-116	5	3
α-helix	120-121	2
β-strand	122	1	4
β-strand	125-129	5	5
β-strand	140-150	11	5
β-strand	151	1	4
β-strand	156-159	4	6
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-176	3	5
β-strand	179-189	11	5
β-strand	198-204	7	6
α-helix	205-207	3
β-strand	209-215	7	6

Chain L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	30-31	2	9
β-strand	36-37	2	9
β-strand	39-44	6	8
β-strand	51-55	5	8
β-strand	59-60	2	8
α-helix	61	1
β-strand	68-73	6	7
β-strand	76-81	6	7
α-helix	86-88	3
β-strand	91-96	6	8
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	116	1	10
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	149-155	7	12
β-strand	158-160	3	12
β-strand	164-168	5	11
β-strand	178-187	10	11
α-helix	188-191	4
β-strand	196-203	8	12
β-strand	210-215	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1	A	protein	424	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), Q92847 (AlphaFold model)
Fab7881 Heavy Chain	H	protein	218	Mus musculus
Fab7881 Light Chain	L	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>6KO5_1 Chimera of Soluble cytochrome b562 and Growth hormone secretagogue receptor type 1 (chains A)
ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKD
FRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLSLGDELLQLFPAPL
LAGVTATCVALFVVGIAGNLLTMLVVSRFRELRTTTNLYLSSMAFSDLLIFLCMPLDLVR
LWQYRPWNFGDLLCKLFQFVSESCTYAKVLTITALSVERYFAICFPLRAKVVVTKGRVKL
VIFVIWAVAFCSAGPIFVLVGVEHEQGTDPWDTNECRPTEFAVRSGLLTVMVWVSSIFFF
LPVFCLTVLYSLIGRKLWRRRRGDAVVGASLRDQNHKQTVKMLAVVVFAFILCWLPFHVG
RYLFSKSFEPGSLEIAQISQYCNLVSFVLFYLSAAINPILYNIMSKKYRVAVFRLLGFEP
FSQR

Sequence of entity 2 (H), FASTA

>6KO5_2 Fab7881 Heavy Chain (chains H)
EVQLQQSGAELVRPGASVKLSCKASGYTFTDYEMHWVKQTPVHGLEWIGAIDPETGGTVY
NQKFKGKATLTADISSTTAYMELRSLTSEDSAVYFCISEDIDESKDYWGQGTTLTVSSAK
TTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (L), FASTA

>6KO5_3 Fab7881 Light Chain (chains L)
DIVMTQSPSSLAVSAGEKVTLSCKSSQSLFNSRTRKNYLAWYQQKPGLSPTLLIYWASTR
KSGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYYLRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
8QX	6-(4-bromanyl-2-fluoranyl-phenoxy)-2-methyl-3-[[(3~{S})-1-propan-2-ylpiperidin-…	C23 H26 Br F N4 O2	1

Primary citation

Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode. Shiimura, Y., Horita, S., Hamamoto, A. et al. Nat Commun (2020) 11:4160-4160. DOI 10.1038/s41467-020-17554-1 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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