MolNFT v1 · #54359 · protein
G117H mutant of human butyrylcholinesterase in complex with echothiophate
2XMD: “G117H mutant of human butyrylcholinesterase in complex with echothiophate”. X-ray diffraction, 10 ligands (DEP, NAG, FUL), 6 pockets (best druggability 0.77). MolNFT v1 #54359 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2XMD
- Type
- protein
- Length
- 527 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholinesterase
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- DEP, NAG, FUL, FUC, NA, CA, UNX, CL, SO4, BR
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 37% helix, 16% strand | P06276 |
Ligands and binding sites
- DEP · Diethyl phosphonate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 21 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- BR · Bromide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.77 | 0.84 | 47 | DEP, NA |
| 2 | 583 | 0.69 | 0.78 | 51 | UNX, CL, BR |
| 3 | 131 | 0.38 | 0.74 | 29 | empty |
| 4 | 66 | 0.37 | 0.78 | 17 | UNX |
| 5 | 90 | 0.36 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 6 glycan, 3 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
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 P06276
- Elsewhere: RCSB PDB 2XMD · PDBe 2XMD · UniProt P06276
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