MolNFT v1 · #117469 · protein
Antibody-bound glucagon-like peptide-1 receptor extracellular domain
5E94 · Antibody Fab fragment light chain: “Antibody-bound glucagon-like peptide-1 receptor extracellular domain”. X-ray diffraction, 11 pockets (best druggability 0.52). MolNFT v1 #117469 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5E94
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; Antibody Fab fragment heavy chain; Glucagon-like…
- UniProt
- P43220
- Pockets
- 11 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antibody Fab fragment light chain | protein | 214 | 7% helix, 50% strand | — |
| B, D | Antibody Fab fragment heavy chain | protein | 224 | 7% helix, 53% strand | — |
| G | Glucagon-like peptide 1 receptor | protein | 110 | 27% helix, 18% strand | P43220 |
| H | Glucagon-like peptide 1 receptor | protein | 100 | 27% helix, 20% strand | P43220 |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.52 | 0.74 | 44 | empty |
| 2 | 131 | 0.46 | 0.77 | 19 | empty |
| 3 | 75 | 0.44 | 0.81 | 16 | empty |
| 4 | 85 | 0.40 | 0.78 | 17 | empty |
| 5 | 89 | 0.39 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2074 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1973 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 859 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 614 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 562 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5E94 · Antibody-bound Glucagon-like Peptide-1 receptor extracellular domain · the same entry in another collection · chain H against H, 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 H against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 5E94 · PDBe 5E94 · UniProt P43220
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