6DKJ: Human GIPR ECD and Fab complex

human GIPR ECD and Fab complex. Determined by X-ray diffraction at 1.95 Å resolution. Released 8 May 2019.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,287
Mol. weight: 121.05 kDa
Released: 8 May 2019

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

Secondary structure: helices and β-sheets

6DKJ contains 53 α-helices and 107 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-99	8	17
β-strand	107-110	4	17
β-strand	114-118	5	17
α-helix	121-123	3
β-strand	124	1	18
α-helix	125-126	2
β-strand	127-131	5	19
α-helix	135-137	3
β-strand	138-139	2	19
β-strand	142-152	11	19
β-strand	153	1	18
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	170-172	3	19
α-helix	173-175	3
β-strand	176-177	2	19
β-strand	183-192	10	19
α-helix	193-195	3
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-13	4	21
β-strand	19-25	7	20
β-strand	33-38	6	21
β-strand	45-49	5	21
β-strand	53-54	2	21
α-helix	55	1
β-strand	62-66	5	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	85-90	6	21
α-helix	96	1
β-strand	97-98	2	21
β-strand	102-106	5	21
β-strand	111	1	22
α-helix	112-113	2
β-strand	114-118	5	23
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	145-150	6	24
β-strand	153-154	2	24
α-helix	155	1
β-strand	159-163	5	23
α-helix	164-166	3
β-strand	167	1	25
β-strand	172	1	25
β-strand	173-182	10	23
α-helix	183-187	5
β-strand	191-197	7	24
β-strand	205-210	6	24

Chain C: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-56	3
β-strand	61	1	13
α-helix	62-63	2
β-strand	64-65	2	14
β-strand	70-71	2	14
β-strand	74	1	13
β-strand	79-83	5	15
α-helix	84-85	2
α-helix	91-94	4
β-strand	98-103	6	15
α-helix	104	1
β-strand	109-114	6	15
α-helix	116-118	3
α-helix	125-128	4

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	32-51	20
α-helix	54-56	3
β-strand	61	1	26
α-helix	62-63	2
β-strand	64-65	2	27
β-strand	70-71	2	27
β-strand	74	1	26
β-strand	79-83	5	28
α-helix	84-85	2
β-strand	98-103	6	28
α-helix	104	1
β-strand	109-114	6	28
α-helix	116-118	3
α-helix	125-133	9

Chain H: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	107-110	4	3
β-strand	114-116	3	3
β-strand	117-118	2	2
α-helix	121-123	3
β-strand	124	1	4
α-helix	125-126	2
β-strand	127-131	5	5
α-helix	135-137	3
β-strand	138-139	2	5
β-strand	142-152	11	5
β-strand	153	1	4
β-strand	158-161	4	6
α-helix	162-164	3
β-strand	166	1	6
β-strand	170-172	3	5
α-helix	173-175	3
β-strand	176-177	2	5
β-strand	183-192	10	5
α-helix	193-195	3
β-strand	202-207	6	6
α-helix	208-210	3
β-strand	212-217	6	6

Chain L: 8 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	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-156	4	11
β-strand	159-163	5	10
α-helix	164-166	3
β-strand	167	1	12
β-strand	172	1	12
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	A, H	protein	223	Homo sapiens	P0DOX5 (AlphaFold model)
Fab light chain	B, L	protein	214	Homo sapiens	V9HW34 (AlphaFold model)
Gastric inhibitory polypeptide receptor	C, D	protein	117	Homo sapiens	P48546 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6DKJ_1 Fab heavy chain (chains A, H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWVRQAPGEGLEWVAAIWFDASDKYY
ADAVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDQAIFGVVPDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, L), FASTA

>6DKJ_2 Fab light chain (chains B, L)
EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGAATRATGIPA
RVSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, D), FASTA

>6DKJ_3 Gastric inhibitory polypeptide receptor (chains C, D)
RAETGSKGQTAGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMYVCWDYAAPNATAR
ASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRDHTQCENPEKNEAFLDQRLILERLQ

Primary citation

Anti-obesity effects of GIPR antagonists alone and in combination with GLP-1R agonists in preclinical models. Killion, E.A., Wang, J., Yie, J. et al. Sci Transl Med (2018) 10. DOI 10.1126/scitranslmed.aat3392 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…
8ECQ 2.0 Å, Bovine Fab 2G3

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