Research workbench
Crystal structure of the lipase LIP_VUT1 from goat rumen metagenome.
Analyse Crystal structure of the lipase LIP_VUT1 from goat rumen metagenome. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NKC
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase, LIP_VUT1
- EC
- 3.1.1.3
- UniProt
- A0A1D8GR37
- Ligands
- CL, AZI
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase, LIP_VUT1 (EC 3.1.1.3) | protein | 171 | 42% helix, 20% strand | A0A1D8GR37 |
| B | Lipase, LIP_VUT1 (EC 3.1.1.3) | protein | 172 | 42% helix, 20% strand | A0A1D8GR37 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- AZI · Azide ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.47 | 0.78 | 24 | empty |
| 2 | 54 | 0.26 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 282 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 6NKC · Crystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome. · 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 A0A1D8GR37
- Elsewhere: RCSB PDB 6NKC · PDBe 6NKC · UniProt A0A1D8GR37
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