Research workbench
Crystal structure of full length human GLP1 receptor in complex with Fab fragment (FAB7F38)
Analyse Crystal structure of full length human GLP1 receptor in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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