Research workbench
Crystal structure of the lipase LIP_VUT4 from goat rumen metagenome.
Analyse Crystal structure of the lipase LIP_VUT4 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
- 6NKF
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIP_VUT4, C3L
- Ligands
- SBT
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIP_VUT4, C3L | protein | 301 | 33% helix, 22% strand | — |
| B, D | LIP_VUT4, C3L | protein | 295 | 35% helix, 22% strand | — |
| C | LIP_VUT4, C3L | protein | 301 | 33% helix, 23% strand | — |
Ligands and binding sites
- SBT · 2-butanol · ligand · chains A, D
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.83 | 0.87 | 96 | empty |
| 2 | 352 | 0.71 | 0.83 | 58 | EDO |
| 3 | 161 | 0.68 | 0.87 | 43 | EDO |
| 4 | 180 | 0.68 | 0.86 | 44 | EDO |
| 5 | 187 | 0.67 | 0.86 | 47 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 2781 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2740 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6NKF · Crystal Structure of the Lipase Lip_vut4 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
- Elsewhere: RCSB PDB 6NKF · PDBe 6NKF
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