MolNFT v1 · #169949 · protein
X-ray structure of the monoclinic crystal form at 1.43 a resolution of lipase from thermomyces (humicola) lanuginosa at 173 K
6XRV: “X-ray structure of the monoclinic crystal form at 1.43 a resolution of lipase from thermomyces (humicola)…”. X-ray diffraction, 5 ligands (OCA, LTV, NAG), 12 pockets (best druggability 0.81). MolNFT v1 #169949 on GenesisL1: 3D…
- PDB
- 6XRV
- Type
- protein
- Length
- 1,614 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- O59952
- Ligands
- OCA, LTV, NAG, CA, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, D, F | Lipase (EC 3.1.1.3) | protein | 269 | 33% helix, 24% strand | O59952 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 6 copies · chains A, D, B, E, C, F
- LTV · 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate · ligand · 6 copies · chains A, D, F, B, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, E, D, F
- CA · Calcium ion · metal · 6 copies · chains B, C, E, D, F
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.81 | 0.82 | 93 | OCA, LTV |
| 2 | 920 | 0.81 | 0.82 | 93 | OCA, LTV |
| 3 | 153 | 0.55 | 0.81 | 28 | empty |
| 4 | 145 | 0.55 | 0.82 | 30 | empty |
| 5 | 370 | 0.55 | 0.74 | 47 | empty |
Interfaces
7 interfaces between chains.
- A–F · 539 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 525 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 515 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 7 covalent, 6 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6XRV · X-ray structure of the monoclinic crystal form at 1.43 A resolution of lipase from… · the same entry in another collection · chain C against C, TM-score 1.00
- O59952 · AlphaFold monomer V2.0 prediction for lipase (O59952) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O59952
- Elsewhere: RCSB PDB 6XRV · PDBe 6XRV · UniProt O59952
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