5V6Y: PDB entry 5V6Y

Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer with bound high-affinity and altered selectivity adrenomedullin variant. Determined by X-ray diffraction at 2.8 Å resolution. Released 31 Jan 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli O157:H7, Homo sapiens
Chains: 8
Atoms: 17,855
Mol. weight: 274.19 kDa
Released: 31 Jan 2018

Explore 5V6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V6Y contains 148 α-helices and 136 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: 36 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	1
α-helix	19-33	15
β-strand	37-40	4	1
α-helix	45-53	9
β-strand	61-65	5	1
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	2
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	3
α-helix	93-98	6
β-strand	100-101	2	4
β-strand	104-105	2	4
β-strand	108-113	6	1
β-strand	116-120	5	5
β-strand	130	1	6
α-helix	134-142	9
β-strand	147-149	3	5
α-helix	156-163	8
β-strand	169-174	6	7
β-strand	177-184	8	7
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	5
α-helix	231-233	3
α-helix	234-239	6
β-strand	244-247	4	5
α-helix	248-250	3
β-strand	251-252	2	6
β-strand	255-256	2	6
α-helix	257	1
α-helix	259	1
β-strand	260-261	2	8
β-strand	262-268	7	1
β-strand	269	1	2
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	1
β-strand	306	1	3
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	8
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-371	13
α-helix	1025-1028	4
α-helix	1030-1035	6
α-helix	1036-1040	5
α-helix	1041-1051	11
α-helix	1053-1055	3
α-helix	1059-1080	22
α-helix	1087-1100	14
α-helix	2036-2054	19
α-helix	2056-2058	3
β-strand	2064-2065	2	9
α-helix	2066-2067	2
β-strand	2068-2069	2	10
β-strand	2074-2075	2	10
β-strand	2078-2079	2	9
β-strand	2082-2087	6	11
α-helix	2088-2089	2
β-strand	2100-2105	6	11
β-strand	2111	1	11
β-strand	2113	1	12
β-strand	2120	1	12
β-strand	2123	1	11
α-helix	2125-2127	3

Chain B: 36 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
α-helix	19-33	15
β-strand	36-40	5	13
α-helix	45-53	9
β-strand	61-65	5	13
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	14
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	15
α-helix	93-98	6
β-strand	100-101	2	16
β-strand	104-105	2	16
β-strand	108-113	6	13
β-strand	116-120	5	17
β-strand	130	1	18
α-helix	134-142	9
β-strand	147-149	3	17
α-helix	156-163	8
β-strand	169-174	6	19
β-strand	177-184	8	19
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	17
α-helix	231-233	3
α-helix	234-239	6
β-strand	244-247	4	17
α-helix	248-250	3
β-strand	251-252	2	18
β-strand	255-256	2	18
α-helix	257	1
α-helix	259	1
β-strand	260-261	2	20
β-strand	262-268	7	13
β-strand	269	1	14
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	13
β-strand	306	1	15
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	20
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-371	13
α-helix	1025-1028	4
α-helix	1030-1035	6
α-helix	1036-1040	5
α-helix	1041-1051	11
α-helix	1053-1055	3
α-helix	1059-1080	22
α-helix	1087-1100	14
α-helix	2037-2054	18
α-helix	2056-2057	2
β-strand	2064-2065	2	21
α-helix	2066-2067	2
β-strand	2068-2069	2	22
β-strand	2074-2075	2	22
β-strand	2078-2079	2	21
β-strand	2082-2087	6	23
α-helix	2088-2089	2
β-strand	2092	1	24
β-strand	2100-2105	6	23
β-strand	2111	1	23
β-strand	2113	1	25
β-strand	2120	1	25
β-strand	2123	1	23
α-helix	2125-2127	3

Chain C: 36 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	26
α-helix	19-33	15
β-strand	37-40	4	26
α-helix	45-52	8
β-strand	61-65	5	26
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	27
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	28
α-helix	93-98	6
β-strand	100-101	2	29
β-strand	104-105	2	29
β-strand	108-113	6	26
β-strand	116-120	5	30
β-strand	130	1	31
α-helix	131-133	3
α-helix	134-142	9
β-strand	147-149	3	30
α-helix	156-163	8
β-strand	172-174	3	32
β-strand	177-179	3	32
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	30
α-helix	231-233	3
α-helix	234-239	6
β-strand	244-247	4	30
α-helix	248-250	3
β-strand	251-252	2	31
β-strand	255-256	2	31
α-helix	257	1
α-helix	259	1
β-strand	260-261	2	33
β-strand	262-268	7	26
β-strand	269	1	27
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	26
β-strand	306	1	28
α-helix	307-314	8
α-helix	317-327	11
β-strand	330-331	2	33
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-369	11
α-helix	1029-1033	5
α-helix	1034-1035	2
α-helix	1036-1040	5
α-helix	1041-1051	11
α-helix	1053-1055	3
α-helix	1063-1080	18
α-helix	1087-1100	14
α-helix	2037-2054	18
α-helix	2056-2058	3
β-strand	2064-2065	2	34
α-helix	2066-2067	2
β-strand	2068-2069	2	35
β-strand	2074-2075	2	35
β-strand	2078-2079	2	34
β-strand	2082-2087	6	36
α-helix	2088-2089	2
β-strand	2095	1	37
β-strand	2100-2105	6	36
β-strand	2111	1	36
β-strand	2113-2114	2	38
β-strand	2119-2120	2	38
β-strand	2123	1	36
β-strand	2128	1	37

Chain D: 35 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	39
α-helix	19-33	15
β-strand	37-40	4	39
α-helix	45-52	8
α-helix	53-55	3
β-strand	61-65	5	39
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	40
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	41
α-helix	93-98	6
β-strand	100-101	2	42
β-strand	104-105	2	42
β-strand	108-113	6	39
β-strand	116-120	5	43
β-strand	130	1	44
α-helix	134-142	9
β-strand	147-149	3	43
α-helix	156-163	8
β-strand	171-174	4	45
β-strand	177-183	7	45
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	43
α-helix	231-233	3
α-helix	234-239	6
β-strand	244-247	4	43
α-helix	248-250	3
β-strand	251-252	2	44
β-strand	255-256	2	44
α-helix	257	1
α-helix	259	1
β-strand	260-261	2	46
β-strand	262-268	7	39
β-strand	269	1	40
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	39
β-strand	306	1	41
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	46
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-371	13
α-helix	1025-1028	4
α-helix	1030-1035	6
α-helix	1036-1040	5
α-helix	1041-1051	11
α-helix	1053-1055	3
α-helix	1059-1080	22
α-helix	1087-1100	14
α-helix	2037-2054	18
β-strand	2064-2065	2	47
α-helix	2066-2067	2
β-strand	2068-2069	2	48
β-strand	2074-2075	2	48
β-strand	2078-2079	2	47
β-strand	2082-2087	6	49
α-helix	2088-2089	2
β-strand	2100-2105	6	49
β-strand	2111	1	49
β-strand	2113	1	50
β-strand	2120	1	50
β-strand	2123	1	49

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	44-47	4

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	39	1	24
α-helix	44-47	4

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	44-47	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related…	A, B, C, D	protein	593	Escherichia coli O157:H7, Homo sapiens	O60894 (AlphaFold model), P0AEX9 (AlphaFold model), Q16602 (AlphaFold model)
ADM	E, F, G, H	protein	17	Homo sapiens	P35318 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5V6Y_1 Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor (chains A, B, C, D)
MAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPD
IIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYN
KDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDI
KDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTS
KVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKP
LGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVD
EALKDAQTNAAAEFTTACQEANYGALLRELCLTQFQVDMEAVGETLWCDWGRTIRSYREL
ADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVGSAGSAGSAEDSIQLGVT
RNKIMTAQYECYQKIMQDPIQQAEGVYCNRTWDGWLCWNDVAAGTESMQLCPDYFQDFDP
SEKVTKICDQDGNWFRHPASNRTWTNYTQCNVNTHEKVKTALNLFYLHHHHHH

Sequence of entity 2 (E, F, G, H), FASTA

>5V6Y_2 ADM (chains E, F, G, H)
DKDNVAPRWLISPWGFX

Primary citation

Probing the Mechanism of Receptor Activity-Modifying Protein Modulation of GPCR Ligand Selectivity through Rational Design of Potent Adrenomedullin and Calcitonin Gene-Related Peptide Antagonists. Booe, J.M., Warner, M.L., Roehrkasse, A.M. et al. Mol Pharmacol (2018) 93:355-367. DOI 10.1124/mol.117.110916 · PubMed

Other PDB entries of the same protein (UniProt O60894 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZHO 1.6 Å, Crystal structure of a CGRP receptor ectodomain heterodimer with bound high affinity…
8AX7 1.65 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
7P0F 1.85 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
8AX6 1.9 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
6D1U 2.05 Å, Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex…
3N7S 2.1 Å, Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR,…
7TYF 2.2 Å, Human Amylin1 Receptor in complex with Gs and rat amylin peptide
9BP3 2.2 Å, Human Amylin1 Receptor in complex with Gs and cagrilintide
7P0I 2.3 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
2YX8 2.4 Å, Crystal structure of the extracellular domain of human RAMP1
9AUC 2.4 Å, Human Amylin1 Receptor in Complex with Gs and human Calcitonin Gene-Related Peptide
4RWG 2.44 Å, Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high…

Browse structure collections

About this viewer

MolViewer shows 5V6Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.