MolNFT v1 · #126946 · protein
BTGH84 mutant with covalent modification by MA3 in complex with pugnac
5MI5 · O-glcnacase BT_4395: “BTGH84 mutant with covalent modification by MA3 in complex with pugnac”. X-ray diffraction, 3 ligands (OAN, 7NQ, CA), 9 pockets (best druggability 0.61). MolNFT v1 #126946 on GenesisL1: 3D structure, binding…
- PDB
- 5MI5
- Type
- protein
- Length
- 677 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase BT_4395
- EC
- 3.2.1.169, 3.2.1.52
- UniProt
- Q89ZI2
- Ligands
- OAN, 7NQ, CA
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 (EC 3.2.1.169, 3.2.1.52) | protein | 677 | 40% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · chains A
- 7NQ · ~{N}-(4-ethoxyquinazolin-2-yl)propanamide · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.61 | 0.78 | 41 | empty |
| 2 | 108 | 0.59 | 0.85 | 21 | OAN |
| 3 | 146 | 0.50 | 0.79 | 20 | empty |
| 4 | 159 | 0.42 | 0.74 | 25 | empty |
| 5 | 70 | 0.37 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5MI5 · BtGH84 mutant with covalent modification by MA3 in complex with PUGNAc · the same entry in another collection · chain A against A, TM-score 1.00
- Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q89ZI2
- Elsewhere: RCSB PDB 5MI5 · PDBe 5MI5 · UniProt Q89ZI2
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