MolNFT v1 · #128812 · protein
Structure of wildtype T.MARITIMA pde (TM1595) with AMP and MN2+
5O1U · Phosphodiesterase: “Structure of wildtype T.MARITIMA pde (TM1595) with AMP and MN2+”. X-ray diffraction, 3 ligands (AMP, MN, CA), 2 pockets (best druggability 0.88). MolNFT v1 #128812 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O1U
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- UniProt
- Q9X1T1
- Ligands
- AMP, MN, CA
- Pockets
- 2 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase | protein | 319 | 43% helix, 19% strand | Q9X1T1 |
| B | Phosphodiesterase | protein | 321 | 43% helix, 19% strand | Q9X1T1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 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 | 1166 | 0.88 | 0.89 | 143 | MN, AMP |
| 2 | 51 | 0.28 | 0.75 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 1923 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5O1U · Structure of wildtype T.maritima PDE (TM1595) with AMP and Mn2+ · 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 5O1U · PDBe 5O1U · UniProt Q9X1T1
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