MolNFT v1 · #168457 · protein
HTR2A bound to 25-cn-nboh in complex with a mini-galpha-Q protein, BETA/GAMMA subunits and an active-state stabilizing single-chain variable fragment (SCFV16) obtained by cryo-electron microscopy (cryoem)
6WHA · Soluble cytochrome B562,5-hydroxytryptamine receptor 2A…: “HTR2A bound to 25-cn-nboh in complex with a mini-galpha-Q protein, BETA/GAMMA subunits and an active-state…”. Electron microscopy, 1 ligand (U0G), 14 pockets (best…
- PDB
- 6WHA
- Type
- protein
- Length
- 1,074 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,5-hydroxytryptamine receptor 2A chimera; G subunit Q (GI2-mini-gq…
- UniProt
- P0ABE7, P28223, P62873, P59768
- Ligands
- U0G
- Pockets
- 14 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562,5-hydroxytryptamine receptor 2A chimera | protein | 244 | 82% helix, 0% strand | P0ABE7, P28223 |
| B | G subunit Q (GI2-mini-gq chimeric) | protein | 211 | 45% helix, 17% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 43% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 51% helix, 0% strand | P59768 |
| E | Single Fab chain (SVFV16) | protein | 230 | 1% helix, 47% strand | — |
Ligands and binding sites
- U0G · 4-(2-{[(2-hydroxyphenyl)methyl]amino}ethyl)-2,5-dimethoxybenzonitrile · ligand · chains A
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 | 1012 | 0.81 | 0.82 | 67 | empty |
| 2 | 704 | 0.78 | 0.83 | 58 | U0G |
| 3 | 133 | 0.75 | 0.93 | 21 | empty |
| 4 | 484 | 0.68 | 0.79 | 65 | empty |
| 5 | 556 | 0.65 | 0.76 | 56 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1966 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1140 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1019 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 529 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 407 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6WHA · HTR2A bound to 25-CN-NBOH in complex with a mini-Galpha-q protein, beta/gamma subunits… · the same entry in another collection · chain E against E, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain C against A, TM-score 0.98
- P28223 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 2A (P28223) · a predicted model of the same protein · chain A against A, TM-score 0.91
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain D against A, TM-score 0.76
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.28
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 P0ABE7
- Every structure of UniProt P28223
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6WHA · PDBe 6WHA · UniProt P0ABE7 · UniProt P28223 · UniProt P62873 · UniProt P59768
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