Research workbench
Structure of wildtype T.MARITIMA pde (TM1595) in ligand-free state
Analyse Structure of wildtype T.MARITIMA pde (TM1595) in ligand-free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O25
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tmpde
- UniProt
- Q9X1T1
- Ligands
- MN, CA
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tmpde | protein | 319 | 44% helix, 19% strand | Q9X1T1 |
| B | Tmpde | protein | 323 | 43% helix, 19% strand | Q9X1T1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
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 | 1134 | 0.86 | 0.87 | 111 | PG4, PEG |
| 2 | 60 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2160 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5O25 · Structure of wildtype T.maritima PDE (TM1595) in ligand-free state · 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 Q9X1T1
- Elsewhere: RCSB PDB 5O25 · PDBe 5O25 · UniProt Q9X1T1
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