Research workbench
Crystal structure of PHOSPHOLIPASE/CARBOXYLESTERASE from dyadobacter fermentans dsm 18053
Analyse Crystal structure of PHOSPHOLIPASE/CARBOXYLESTERASE from dyadobacter fermentans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H0C
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHOSPHOLIPASE/CARBOXYLESTERASE
- UniProt
- C6VYE5
- Ligands
- NA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHOSPHOLIPASE/CARBOXYLESTERASE | protein | 210 | 35% helix, 22% strand | C6VYE5 |
| B | PHOSPHOLIPASE/CARBOXYLESTERASE | protein | 209 | 36% helix, 22% strand | C6VYE5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.67 | 0.80 | 48 | CIT, GOL |
| 2 | 107 | 0.51 | 0.82 | 24 | CIT |
| 3 | 103 | 0.38 | 0.75 | 20 | empty |
| 4 | 52 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 452 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4H0C · Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053 · 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 C6VYE5
- Elsewhere: RCSB PDB 4H0C · PDBe 4H0C · UniProt C6VYE5
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