Research workbench
Crystal structure of the phosphatase domain of C. thermocellum (bacterial) pnkp
Analyse Crystal structure of the phosphatase domain of C. thermocellum (bacterial) pnkp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J6O
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase
- EC
- 3.1.3.16
- UniProt
- A3DJ38
- Ligands
- MN
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallophosphoesterase (EC 3.1.3.16) | protein | 261 | 29% helix, 23% strand | A3DJ38 |
| B | Metallophosphoesterase (EC 3.1.3.16) | protein | 258 | 30% helix, 24% strand | A3DJ38 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.58 | 0.77 | 39 | empty |
| 2 | 141 | 0.42 | 0.75 | 24 | GOL, MN, CIT |
| 3 | 56 | 0.36 | 0.79 | 16 | empty |
| 4 | 61 | 0.32 | 0.76 | 17 | empty |
| 5 | 53 | 0.30 | 0.76 | 16 | MN, CIT |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J6O · Crystal Structure of the Phosphatase Domain of C. thermocellum (Bacterial) PnkP · 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 A3DJ38
- Elsewhere: RCSB PDB 4J6O · PDBe 4J6O · UniProt A3DJ38
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