MolNFT v1 · #97572 · protein
Crystal structure of the eal domain of C-di-gmp specific phosphodiesterase yaha
4KIE · Cyclic di-gmp phosphodiesterase yaha: “Crystal structure of the eal domain of C-di-gmp specific phosphodiesterase yaha”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #97572 on GenesisL1: 3D structure, binding…
- PDB
- 4KIE
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic di-gmp phosphodiesterase yaha
- EC
- 3.1.4.-
- UniProt
- P21514
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic di-gmp phosphodiesterase yaha (EC 3.1.4.-) | protein | 261 | 45% helix, 22% strand | P21514 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.68 | 0.92 | 16 | PGE |
| 2 | 341 | 0.68 | 0.81 | 45 | PGE |
| 3 | 57 | 0.35 | 0.78 | 13 | PGE |
Compared structures
- 4KIE · Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA · the same entry in another collection · chain A against A, TM-score 1.00
- P21514 · AlphaFold monomer V2.0 prediction for cyclic di-gmp phosphodiesterase pdel (P21514) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P21514
- Elsewhere: RCSB PDB 4KIE · PDBe 4KIE · UniProt P21514
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.