MolNFT v1 · #141621 · protein
The complex structure of fomd with cdp
5ZDN: “The complex structure of fomd with cdp”. X-ray diffraction, 2 ligands (CDP, MG), 2 pockets (best druggability 0.56). MolNFT v1 #141621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZDN
- Type
- protein
- Length
- 192 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fomd
- UniProt
- D2SNF7
- Ligands
- CDP, MG
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fomd | protein | 192 | 20% helix, 36% strand | D2SNF7 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.56 | 0.78 | 37 | CDP, MG, GOL |
| 2 | 61 | 0.35 | 0.78 | 21 | empty |
Compared structures
- 5ZDN · The complex structure of FomD with CDP · 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 D2SNF7
- Elsewhere: RCSB PDB 5ZDN · PDBe 5ZDN · UniProt D2SNF7
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