MolNFT v1 · #93529 · protein
Crystal structure of the diguanylate cyclase dgcz
4H54 · Diguanylate cyclase ydeh: “Crystal structure of the diguanylate cyclase dgcz”. X-ray diffraction, 4 ligands (GAV, C2E, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #93529 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4H54
- Type
- protein
- Length
- 543 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase ydeh
- EC
- 2.7.7.65
- UniProt
- P31129
- Ligands
- GAV, C2E, ZN, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diguanylate cyclase ydeh (EC 2.7.7.65) | protein | 274 | 59% helix, 16% strand | P31129 |
| B | Diguanylate cyclase ydeh (EC 2.7.7.65) | protein | 269 | 59% helix, 16% strand | P31129 |
Ligands and binding sites
- GAV · Guanosine-5'-rp-alpha-thio-triphosphate · ligand · 4 copies · chains A, B
- 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 · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.78 | 0.80 | 74 | GAV |
| 2 | 376 | 0.65 | 0.79 | 43 | empty |
| 3 | 144 | 0.61 | 0.85 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2097 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 P31129
- Elsewhere: RCSB PDB 4H54 · PDBe 4H54 · UniProt P31129
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