Research workbench
Cryoem structure of inactive H2R bound to famotidine, NB6M, and nabfab
Analyse Cryoem structure of inactive H2R bound to famotidine, NB6M, and nabfab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UL3
- Type
- protein
- Length
- 767 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histamine H2 receptor; Nanobody 6M; Nabfab hc; Nabfab lc
- UniProt
- P25021, A0A8B8VNB6
- Ligands
- FO9
- Pockets
- 7 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histamine H2 receptor | protein | 268 | 80% helix, 0% strand | P25021, A0A8B8VNB6 |
| C | Nanobody 6M | protein | 117 | 3% helix, 54% strand | — |
| H | Nabfab hc | protein | 183 | 5% helix, 44% strand | — |
| L | Nabfab lc | protein | 199 | 6% helix, 46% strand | — |
Ligands and binding sites
- FO9 · famotidine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.78 | 0.86 | 61 | FO9 |
| 2 | 96 | 0.50 | 0.82 | 21 | empty |
| 3 | 72 | 0.46 | 0.82 | 16 | empty |
| 4 | 178 | 0.43 | 0.73 | 31 | empty |
| 5 | 58 | 0.37 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1761 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 732 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 4 hydrogen bonds · protein-protein
- C–L · 191 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7UL3 · CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab · the same entry in another collection · chain A against A, TM-score 1.00
- P25021 · AlphaFold monomer V2.0 prediction for histamine H2 receptor (P25021) · a predicted model of the same protein · chain A 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 P25021
- Every structure of UniProt A0A8B8VNB6
- Elsewhere: RCSB PDB 7UL3 · PDBe 7UL3 · UniProt P25021 · UniProt A0A8B8VNB6
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