MolNFT v1 · #137133 · protein
Structure of the human glp-1 receptor complex with NNC0640
5VEX · Glucagon-like peptide 1 receptor, endolysin chimera: “Structure of the human glp-1 receptor complex with NNC0640”. X-ray diffraction, 1 ligand (97V), 14 pockets (best druggability 0.70). MolNFT v1 #137133 on GenesisL1: 3D structure…
- PDB
- 5VEX
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon-like peptide 1 receptor, endolysin chimera
- EC
- 3.2.1.17
- UniProt
- P43220, P00720
- Ligands
- 97V
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucagon-like peptide 1 receptor, endolysin chimera (EC 3.2.1.17) | protein | 423 | 74% helix, 3% strand | P43220, P00720 |
Ligands and binding sites
- 97V · 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl) phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl) benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.70 | 0.76 | 77 | empty |
| 2 | 550 | 0.66 | 0.76 | 56 | empty |
| 3 | 237 | 0.61 | 0.81 | 29 | empty |
| 4 | 207 | 0.60 | 0.81 | 27 | empty |
| 5 | 204 | 0.58 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 576 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 5VEX · Structure of the human GLP-1 receptor complex with NNC0640 · the same entry in another collection · chain A against A, TM-score 1.00
- P43220 · AlphaFold monomer V2.0 prediction for glucagon-like peptide 1 receptor (P43220) · a predicted model of the same protein · chain A against A, TM-score 0.56
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 P43220
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 5VEX · PDBe 5VEX · UniProt P43220 · UniProt P00720
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