MolNFT v1 · #54659 · protein
Structure of the extracellular domain of human RAMP2
2XVT · Receptor activity-modifying protein 2: “Structure of the extracellular domain of human RAMP2”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.82). MolNFT v1 #54659 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XVT
- Type
- protein
- Length
- 469 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor activity-modifying protein 2
- UniProt
- O60895
- Ligands
- CA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Receptor activity-modifying protein 2 | protein | 78 | 74% helix, 0% strand | O60895 |
| C, F | Receptor activity-modifying protein 2 | protein | 79 | 73% helix, 0% strand | O60895 |
| D | Receptor activity-modifying protein 2 | protein | 79 | 73% helix, 0% strand | O60895 |
| E | Receptor activity-modifying protein 2 | protein | 76 | 76% helix, 0% strand | O60895 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains C, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.82 | 0.84 | 84 | CA |
| 2 | 128 | 0.40 | 0.74 | 14 | empty |
| 3 | 123 | 0.38 | 0.73 | 16 | empty |
Interfaces
8 interfaces between chains.
- B–D · 883 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 711 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 702 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 694 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 693 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2XVT · Structure of the extracellular domain of human RAMP2 · the same entry in another collection · chain F against F, TM-score 1.00
- O60895 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 2 (O60895) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 O60895
- Elsewhere: RCSB PDB 2XVT · PDBe 2XVT · UniProt O60895
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