MolNFT v1 · #145912 · protein
Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex with adrenomedullin 2/INTERMEDIN
6D1U · Maltose-binding periplasmic PROTEIN,RECEPTOR activity…: “Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex with adrenomedullin…”. X-ray diffraction, 3 ligands (GLC, NA, NH2), 20 pockets (best…
- PDB
- 6D1U
- Type
- protein
- Length
- 1,715 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
- P0AEY0, O60894, Q16602
- Ligands
- GLC, NA, NH2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 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 | 553 | 45% helix, 18% strand | P0AEY0, O60894, Q16602 |
| B | Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor | protein | 553 | 45% helix, 18% strand | P0AEY0, O60894, Q16602 |
| C | Maltose-binding periplasmic PROTEIN,RECEPTOR activity- modifying protein 1,CALCITONIN gene-related peptide type 1 receptor | protein | 567 | 47% helix, 18% strand | P0AEY0, O60894, Q16602 |
| D, F | ADM2 | protein | 13 | 0% helix, 0% strand | — |
| E | ADM2 | protein | 16 | 0% helix, 6% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, C
- 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
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.79 | 0.83 | 89 | GLC |
| 2 | 549 | 0.79 | 0.85 | 68 | GLC |
| 3 | 995 | 0.78 | 0.80 | 113 | GLC |
| 4 | 241 | 0.63 | 0.82 | 58 | empty |
| 5 | 536 | 0.62 | 0.75 | 55 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1000 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 848 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 796 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 6D1U · Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex with… · 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 C 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 A against A, TM-score 0.17
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
- Elsewhere: RCSB PDB 6D1U · PDBe 6D1U · UniProt P0AEY0 · UniProt O60894 · UniProt Q16602
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