MolNFT v1 · #158114 · protein
Crystal structure of the lipase LIP_VUT3 from goat rumen metagenome.
6NKD · LIP_VUT3, C2L: “Crystal structure of the lipase LIP_VUT3 from goat rumen metagenome.”. X-ray diffraction, 2 ligands (SO4, CL), 3 pockets (best druggability 0.76). MolNFT v1 #158114 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NKD
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIP_VUT3, C2L
- UniProt
- Q65NA4
- Ligands
- SO4, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | LIP_VUT3, C2L | protein | 210 | 54% helix, 14% strand | Q65NA4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.76 | 0.82 | 50 | SO4, FMT |
| 2 | 73 | 0.68 | 0.93 | 18 | empty |
| 3 | 94 | 0.66 | 0.91 | 23 | CL |
Interfaces
1 interface between chains.
- A–B · 962 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 6NKD · Crystal Structure of the Lipase Lip_vut3 from Goat Rumen metagenome. · the same entry in another collection · chain A against A, TM-score 1.00
- Q65NA4 · AlphaFold monomer V2.0 prediction for spore germination lipase lipc (Q65NA4) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q65NA4
- Elsewhere: RCSB PDB 6NKD · PDBe 6NKD · UniProt Q65NA4
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