MolNFT v1 · #50272 · protein
Crystal structure of VCA0042 complexed with C-di-gmp
2RDE · Uncharacterized protein VCA0042: “Crystal structure of VCA0042 complexed with C-di-gmp”. X-ray diffraction, 1 ligand (C2E), 4 pockets (best druggability 0.75). MolNFT v1 #50272 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2RDE
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein VCA0042
- UniProt
- A5F1K1
- Ligands
- C2E
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein VCA0042 | protein | 224 | 10% helix, 52% strand | A5F1K1 |
| B | Uncharacterized protein VCA0042 | protein | 225 | 10% helix, 53% strand | A5F1K1 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.75 | 0.78 | 102 | empty |
| 2 | 90 | 0.42 | 0.79 | 19 | C2E |
| 3 | 74 | 0.41 | 0.80 | 16 | C2E |
| 4 | 90 | 0.34 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1453 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2RDE · Crystal structure of VCA0042 complexed with c-di-GMP · the same entry in another collection · chain A against A, TM-score 1.00
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 A5F1K1
- Elsewhere: RCSB PDB 2RDE · PDBe 2RDE · UniProt A5F1K1
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