MolNFT v1 · #107866 · protein
Open conformation of O. piceae sterol esterase mutant I544W
4UPD: “Open conformation of O. piceae sterol esterase mutant I544W”. X-ray diffraction, 2 ligands (7P9, NAG), 8 pockets (best druggability 0.73). MolNFT v1 #107866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UPD
- Type
- protein
- Length
- 1,075 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol esterase
- EC
- 3.1.1.13
- UniProt
- Q2TFW1
- Ligands
- 7P9, NAG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol esterase (EC 3.1.1.13) | protein | 538 | 38% helix, 17% strand | Q2TFW1 |
| B | Sterol esterase (EC 3.1.1.13) | protein | 537 | 37% helix, 16% strand | Q2TFW1 |
Ligands and binding sites
- 7P9 · [(2R)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.73 | 0.81 | 58 | empty |
| 2 | 479 | 0.71 | 0.80 | 57 | PGE |
| 3 | 207 | 0.58 | 0.80 | 34 | empty |
| 4 | 92 | 0.41 | 0.78 | 19 | empty |
| 5 | 89 | 0.41 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 787 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4UPD · Open conformation of O. piceae sterol esterase mutant I544W · 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 Q2TFW1
- Elsewhere: RCSB PDB 4UPD · PDBe 4UPD · UniProt Q2TFW1
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