MolNFT v1 · #120810 · protein
Structure of esterase EST22
5HC4 · Lipolytic enzyme: “Structure of esterase EST22”. X-ray diffraction, 17 pockets (best druggability 0.77). MolNFT v1 #120810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HC4
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipolytic enzyme
- EC
- 3.1.1.-
- UniProt
- H6BDX1
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipolytic enzyme (EC 3.1.1.-) | protein | 341 | 40% helix, 18% strand | H6BDX1 |
| C | Lipolytic enzyme (EC 3.1.1.-) | protein | 340 | 41% helix, 20% strand | H6BDX1 |
| D | Lipolytic enzyme (EC 3.1.1.-) | protein | 342 | 39% helix, 20% strand | H6BDX1 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.77 | 0.84 | 46 | empty |
| 2 | 709 | 0.76 | 0.81 | 70 | GOL, TRS |
| 3 | 505 | 0.75 | 0.83 | 51 | empty |
| 4 | 542 | 0.75 | 0.82 | 48 | empty |
| 5 | 785 | 0.73 | 0.78 | 109 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1140 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 138 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HC4 · Structure of esterase Est22 · 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 H6BDX1
- Elsewhere: RCSB PDB 5HC4 · PDBe 5HC4 · UniProt H6BDX1
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