MolNFT v1 · #106346 · protein
Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high affinity cgrp analog
4RWG · Maltose-binding periplasmic protein, receptor activity…: “Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high affinity cgrp analog”. X-ray diffraction, 3 ligands (GLC, MG, NH2), 18 pockets (best…
- PDB
- 4RWG
- Type
- protein
- Length
- 1,704 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, receptor activity- modifying protein 1, calcitonin…
- UniProt
- P0AEX9, O60894, Q16602
- Ligands
- GLC, MG, NH2
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 46% 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 fusion protein | protein | 557 | 46% helix, 18% strand | P0AEX9, O60894, Q16602 |
| B | Maltose-binding periplasmic protein, receptor activity- modifying protein 1, calcitonin gene-related peptide type 1 receptor fusion protein | protein | 569 | 47% helix, 18% strand | P0AEX9, O60894, Q16602 |
| C | Maltose-binding periplasmic protein, receptor activity- modifying protein 1, calcitonin gene-related peptide type 1 receptor fusion protein | protein | 546 | 46% helix, 19% strand | P0AEX9, O60894, Q16602 |
| D, E | Cgrp analog | protein | 11 | 0% helix, 0% strand | — |
| F | Cgrp analog | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- MG · Magnesium ion · metal · chains B
- NH2 · Amino group · ion · 3 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.80 | 0.82 | 85 | GLC |
| 2 | 1198 | 0.79 | 0.80 | 136 | GLC |
| 3 | 1189 | 0.77 | 0.79 | 127 | GLC |
| 4 | 140 | 0.61 | 0.85 | 22 | empty |
| 5 | 474 | 0.61 | 0.75 | 51 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1101 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 869 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 745 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 735 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4RWG · Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high… · the same entry in another collection · chain F against F, TM-score 1.00
- Q16602 · AlphaFold monomer V2.0 prediction for calcitonin gene-related peptide type 1 receptor… · a predicted model of the same protein · chain B against A, TM-score 0.23
- O60894 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 1 (O60894) · a predicted model of the same protein · chain C against A, TM-score 0.18
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 P0AEX9
- Every structure of UniProt O60894
- Every structure of UniProt Q16602
- Elsewhere: RCSB PDB 4RWG · PDBe 4RWG · UniProt P0AEX9 · UniProt O60894 · UniProt Q16602
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