Research workbench
Lipase (open form)
Analyse Lipase (open form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KHM
- Type
- protein
- Length
- 8,053 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, ALPHA/BETA domain protein
- UniProt
- E6DAE5
- Ligands
- DKF, DKL, DK6, DKO, DK9
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J, N, O, P, S, U, W | Hydrolase, ALPHA/BETA domain protein | protein | 310 | 44% helix, 16% strand | E6DAE5 |
| B, C, H, M, R, T, V, X, Y, Z | Hydrolase, ALPHA/BETA domain protein | protein | 309 | 43% helix, 17% strand | E6DAE5 |
| D, F | Hydrolase, ALPHA/BETA domain protein | protein | 308 | 43% helix, 17% strand | E6DAE5 |
| E, I, Q | Hydrolase, ALPHA/BETA domain protein | protein | 311 | 42% helix, 16% strand | E6DAE5 |
| K, L | Hydrolase, ALPHA/BETA domain protein | protein | 312 | 42% helix, 17% strand | E6DAE5 |
Ligands and binding sites
- DKF · hexane-1,1-diol · ligand · 11 copies · chains E, G, I, J, K, L, M, U, V, Y, W
- DKL · heptane-1,1-diol · ligand · 5 copies · chains A, C, Q, T, X
- DK6 · propane-1,1-diol · ligand · 4 copies · chains D, H, S, Z
- DKO · octane-1,1-diol · ligand · 3 copies · chains B, N, R
- DK9 · pentane-1,1-diol · ligand · 3 copies · chains F, O, P
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 | 467 | 0.83 | 0.90 | 64 | empty |
| 2 | 430 | 0.83 | 0.91 | 63 | empty |
| 3 | 452 | 0.82 | 0.90 | 65 | empty |
| 4 | 772 | 0.80 | 0.84 | 102 | empty |
| 5 | 261 | 0.80 | 0.91 | 36 | empty |
Interfaces
38 interfaces between chains.
- K–L · 1225 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 18 hydrogen bonds · protein-protein
- S–T · 1220 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1216 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1215 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 covalent (covalent ligand).
Compared structures
- 6KHM · Lipase (Open form) · the same entry in another collection · chain B against B, 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 E6DAE5
- Elsewhere: RCSB PDB 6KHM · PDBe 6KHM · UniProt E6DAE5
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