Research workbench
Human secr in complex with an engineered gs heterotrimer
Analyse Human secr in complex with an engineered gs heterotrimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3S
- Type
- protein
- Length
- 1,048 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secretin; Secretin receptor; Guanine nucleotide-binding protein G(S) subunit alpha…
- UniProt
- P09683, P47872, P63092, P54311, P63212
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Secretin | protein | 27 | 93% helix, 0% strand | P09683 |
| R | Secretin receptor | protein | 266 | 80% helix, 0% strand | P47872 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 230 | 46% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 45% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 49% helix, 0% strand | P63212 |
| N | Nanobody NB35 | protein | 128 | 7% helix, 43% strand | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.81 | 0.86 | 52 | empty |
| 2 | 782 | 0.75 | 0.80 | 59 | empty |
| 3 | 967 | 0.75 | 0.78 | 72 | empty |
| 4 | 152 | 0.71 | 0.90 | 25 | empty |
| 5 | 342 | 0.70 | 0.83 | 50 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2141 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1493 Ų buried · 22 hydrogen bonds · protein-protein
- R–A · 1080 Ų buried · 10 hydrogen bonds · protein-protein
- P–R · 1055 Ų buried · 10 hydrogen bonds · protein-protein
- A–N · 858 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7D3S · Human SECR in complex with an engineered Gs heterotrimer · the same entry in another collection · chain N against N, TM-score 1.00
- P54311 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P47872 · AlphaFold monomer V2.0 prediction for secretin receptor (P47872) · a predicted model of the same protein · chain R against A, TM-score 0.98
- P09683 · AlphaFold monomer V2.0 prediction for secretin (P09683) · a predicted model of the same protein · chain P against A, TM-score 0.84
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.68
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 P09683
- Every structure of UniProt P47872
- Every structure of UniProt P63092
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7D3S · PDBe 7D3S · UniProt P09683 · UniProt P47872 · UniProt P63092 · UniProt P54311 · UniProt P63212
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