MolNFT v1 · #155914 · protein
Crystal structure of full length human GLP1 receptor in complex with Fab fragment (FAB7F38)
6LN2 · Glucagon-like peptide 1 RECEPTOR,RUBREDOXIN,GLUCAGON-like…: “Crystal structure of full length human GLP1 receptor in complex with Fab fragment (FAB7F38)”. X-ray diffraction, 3 ligands (97Y, NAG, ZN), 9 pockets (best druggability…
- PDB
- 6LN2
- Type
- protein
- Length
- 876 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon-like peptide 1 RECEPTOR,RUBREDOXIN,GLUCAGON-like peptide 1 receptor…
- UniProt
- P43220, P00268
- Ligands
- 97Y, NAG, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucagon-like peptide 1 RECEPTOR,RUBREDOXIN,GLUCAGON-like peptide 1 receptor | protein | 437 | 61% helix, 5% strand | P43220, P00268 |
| B | FAB7F38_LIGHT chain | protein | 213 | 4% helix, 51% strand | — |
| C | FAB7F38_HEAVY chain | protein | 226 | 5% helix, 46% strand | — |
Ligands and binding sites
- 97Y · N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, C
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.76 | 0.79 | 77 | empty |
| 2 | 414 | 0.64 | 0.78 | 50 | empty |
| 3 | 335 | 0.60 | 0.77 | 38 | empty |
| 4 | 152 | 0.45 | 0.76 | 24 | empty |
| 5 | 59 | 0.44 | 0.83 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1933 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 628 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6LN2 · Crystal structure of full length human GLP1 receptor in complex with Fab fragment… · 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 0.61
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.12
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 P00268
- Elsewhere: RCSB PDB 6LN2 · PDBe 6LN2 · UniProt P43220 · UniProt P00268
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