MolNFT v1 · #16536 · protein
Crystal structure of glycerophosphodiester phosphodiesterase (gdpd) (TM1621) from thermotoga maritima at 1.60 a resolution
1O1Z: “Crystal structure of glycerophosphodiester phosphodiesterase (gdpd) (TM1621) from thermotoga maritima at 1.60…”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.54). MolNFT v1 #16536 on GenesisL1: 3D structure…
- PDB
- 1O1Z
- Type
- protein
- Length
- 226 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphodiester phosphodiesterase
- EC
- 3.1.4.46
- UniProt
- Q9X1V6
- Ligands
- NA
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerophosphodiester phosphodiesterase (EC 3.1.4.46) | protein | 226 | 41% helix, 23% strand | Q9X1V6 |
Ligands and binding sites
- NA · Sodium ion · metal · 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 | 121 | 0.54 | 0.82 | 17 | empty |
Compared structures
- 1O1Z · Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from… · 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 Q9X1V6
- Elsewhere: RCSB PDB 1O1Z · PDBe 1O1Z · UniProt Q9X1V6
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