Research workbench
Crystal structure of extracellular lipase lipa from serratia marcescens
Analyse Crystal structure of extracellular lipase lipa from serratia marcescens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QUB
- Type
- protein
- Length
- 3,690 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular lipase
- EC
- 3.1.1.3
- UniProt
- Q59933
- Ligands
- CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Extracellular lipase (EC 3.1.1.3) | protein | 615 | 26% helix, 26% strand | Q59933 |
Ligands and binding sites
- CA · Calcium ion · metal · 48 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.72 | 0.76 | 94 | empty |
| 2 | 536 | 0.71 | 0.79 | 44 | empty |
| 3 | 553 | 0.71 | 0.79 | 43 | empty |
| 4 | 535 | 0.70 | 0.79 | 45 | empty |
| 5 | 562 | 0.70 | 0.78 | 42 | empty |
Interfaces
11 interfaces between chains.
- A–E · 459 Ų buried · 9 hydrogen bonds · protein-protein
- C–I · 424 Ų buried · 5 hydrogen bonds · protein-protein
- I–K · 422 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 385 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 378 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2QUB · Crystal structure of extracellular lipase LipA from Serratia marcescens · the same entry in another collection · chain E against E, 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 Q59933
- Elsewhere: RCSB PDB 2QUB · PDBe 2QUB · UniProt Q59933
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