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Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer with bound high-affinity and altered selectivity adrenomedullin variant

Analyse Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5V6Y
Type: protein
Length: 2,253 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN…
UniProt: P0AEY0, O60894, Q16602, P35318
Ligands: GLC, NH2
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor	protein	550	46% helix, 18% strand	P0AEY0, O60894, Q16602
B	Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor	protein	551	45% helix, 19% strand	P0AEY0, O60894, Q16602
C	Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor	protein	549	44% helix, 18% strand	P0AEY0, O60894, Q16602
D	Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor	protein	547	46% helix, 18% strand	P0AEY0, O60894, Q16602
E, F	Adm	protein	15	27% helix, 0% strand	P35318
G, H	Adm	protein	13	0% helix, 0% strand	P35318

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
NH2 · Amino group · ion · 4 copies · chains A, E, B, F, C, G, D, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	892	0.81	0.83	89	empty
2	1175	0.80	0.82	90	GLC
3	978	0.80	0.81	110	GLC
4	1088	0.79	0.81	115	empty
5	701	0.78	0.83	69	GLC

Interfaces

9 interfaces between chains.

C–G · 1149 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1097 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 987 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 949 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 871 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

5V6Y · Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer with bound… · the same entry in another collection · chain A against A, TM-score 1.00
P35318 · AlphaFold monomer V2.0 prediction for pro-adrenomedullin (P35318) · a predicted model of the same protein · chain H against A, TM-score 0.41

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0AEY0
Every structure of UniProt O60894
Every structure of UniProt Q16602
Every structure of UniProt P35318
Elsewhere: RCSB PDB 5V6Y · PDBe 5V6Y · UniProt P0AEY0 · UniProt O60894 · UniProt Q16602 · UniProt P35318

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