Research workbench
Crystal structure of pseudomonas sp. MIS38 lipase (pml) in the open conformation following dialysis against ca-free buffer
Analyse Crystal structure of pseudomonas sp. MIS38 lipase (pml) in the open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A6Z
- Type
- protein
- Length
- 1,229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- Q9RBY1
- Ligands
- CA
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase (EC 3.1.1.3) | protein | 613 | 28% helix, 25% strand | Q9RBY1 |
| C | Lipase (EC 3.1.1.3) | protein | 616 | 26% helix, 26% strand | Q9RBY1 |
Ligands and binding sites
- CA · Calcium ion · metal · 17 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.74 | 0.88 | 26 | empty |
| 2 | 196 | 0.72 | 0.88 | 24 | empty |
| 3 | 115 | 0.68 | 0.90 | 21 | empty |
| 4 | 111 | 0.67 | 0.90 | 21 | empty |
| 5 | 271 | 0.59 | 0.79 | 44 | empty |
Interfaces
1 interface between chains.
- A–C · 1018 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A6Z · Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation… · 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 Q9RBY1
- Elsewhere: RCSB PDB 3A6Z · PDBe 3A6Z · UniProt Q9RBY1
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