MolNFT v1 · #139055 · protein
Crystal structure of hep-cmp-bound form of cytidylyltransferase (cytase) domain of FOM1 from streptomyces wedmorensis
5X3D · Phosphoenolpyruvate phosphomutase: “Crystal structure of hep-cmp-bound form of cytidylyltransferase (cytase) domain of FOM1 from streptomyces…”. X-ray diffraction, 1 ligand (7XL), 1 pocket (best druggability 0.62). MolNFT v1 #139055…
- PDB
- 5X3D
- Type
- protein
- Length
- 126 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate phosphomutase
- UniProt
- P96074
- Ligands
- 7XL
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate phosphomutase | protein | 126 | 39% helix, 24% strand | P96074 |
Ligands and binding sites
- 7XL · [[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.62 | 0.81 | 33 | 7XL |
Compared structures
- 5X3D · Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1… · the same entry in another collection · chain A against A, TM-score 1.00
- P96074 · AlphaFold monomer V2.0 prediction for fosfomycin biosynthesis bifunctional protein FOM1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P96074
- Elsewhere: RCSB PDB 5X3D · PDBe 5X3D · UniProt P96074
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