MolNFT v1 · #38377 · protein
Complex of gs- with the catalytic domains of mammalian adenylyl cyclase: complex with tnp-ATP and mn
2GVD · Adenylate cyclase type 5: “Complex of gs- with the catalytic domains of mammalian adenylyl cyclase: complex with tnp-ATP and mn”. X-ray diffraction, 5 ligands (FKP, 128, GSP), 6 pockets (best druggability 0.78). MolNFT v1 #38377 on…
- PDB
- 2GVD
- Type
- protein
- Length
- 701 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate cyclase type 5; Adenylate cyclase type 2; Guanine nucleotide-binding protein…
- EC
- 4.6.1.1
- UniProt
- P30803, P26769, P04896
- Ligands
- FKP, 128, GSP, MN, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate cyclase type 5 (EC 4.6.1.1) | protein | 190 | 37% helix, 27% strand | P30803 |
| B | Adenylate cyclase type 2 (EC 4.6.1.1) | protein | 189 | 35% helix, 32% strand | P26769 |
| C | Guanine nucleotide-binding protein G(S), alpha subunit | protein | 322 | 47% helix, 10% strand | P04896 |
Ligands and binding sites
- FKP · Methylpiperazinoforskolin · ligand · chains A, B
- 128 · Spiro(2,4,6-trinitrobenzene[1,2a]-2O',3O'-methylene-adenine-triphosphate · ligand · chains A, B
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · chains C
- MN · Manganese (II) ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.78 | 0.85 | 71 | MN, CL, GSP |
| 2 | 927 | 0.74 | 0.78 | 66 | MN, FKP, 128 |
| 3 | 123 | 0.38 | 0.74 | 23 | empty |
| 4 | 58 | 0.35 | 0.78 | 14 | empty |
| 5 | 55 | 0.33 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1868 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 847 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 248 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2GVD · Complex Of Gs- With The Catalytic Domains Of Mammalian Adenylyl Cyclase: Complex With… · the same entry in another collection · chain A against A, TM-score 1.00
- P04896 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P26769 · AlphaFold monomer V2.0 prediction for adenylate cyclase type 2 (P26769) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P30803 · AlphaFold monomer V2.0 prediction for adenylate cyclase type 5 (P30803) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P30803
- Every structure of UniProt P26769
- Every structure of UniProt P04896
- Elsewhere: RCSB PDB 2GVD · PDBe 2GVD · UniProt P30803 · UniProt P26769 · UniProt P04896
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