MolNFT v1 · #120808 · protein
Structure of esterase EST22 mutant-S188A with P-nitrophenol
5HC2 · Lipolytic enzyme: “Structure of esterase EST22 mutant-S188A with P-nitrophenol”. X-ray diffraction, 1 ligand (NPO), 12 pockets (best druggability 0.83). MolNFT v1 #120808 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HC2
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipolytic enzyme
- EC
- 3.1.1.-
- UniProt
- H6BDX1
- Ligands
- NPO
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Lipolytic enzyme (EC 3.1.1.-) | protein | 343 | 39% helix, 18% strand | H6BDX1 |
| B | Lipolytic enzyme (EC 3.1.1.-) | protein | 342 | 40% helix, 18% strand | H6BDX1 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.83 | 0.84 | 120 | NPO, IMD |
| 2 | 544 | 0.79 | 0.85 | 48 | NPO, IMD |
| 3 | 555 | 0.78 | 0.84 | 47 | NPO, IMD |
| 4 | 1059 | 0.75 | 0.78 | 131 | empty |
| 5 | 101 | 0.46 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1151 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 147 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 143 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HC2 · Structure of esterase Est22 mutant-S188A with p-nitrophenol · 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 5HC2 · PDBe 5HC2 · UniProt H6BDX1
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