MolNFT v1 · #126948 · protein
BTGH84 mutant with covalent modification by MA4 in complex with pugnac
5MI7 · O-glcnacase BT_4395: “BTGH84 mutant with covalent modification by MA4 in complex with pugnac”. X-ray diffraction, 3 ligands (OAN, 7NT, CA), 8 pockets (best druggability 0.62). MolNFT v1 #126948 on GenesisL1: 3D structure, binding…
- PDB
- 5MI7
- Type
- protein
- Length
- 671 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, 7NT, CA
- Pockets
- 8 · best druggability 0.62
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 | 671 | 40% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · chains A
- 7NT · ~{N}-(4-morpholin-4-ylthieno[2,3-d]pyrimidin-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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.62 | 0.78 | 46 | empty |
| 2 | 90 | 0.55 | 0.85 | 19 | OAN |
| 3 | 200 | 0.45 | 0.73 | 32 | empty |
| 4 | 104 | 0.38 | 0.76 | 22 | empty |
| 5 | 79 | 0.36 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5MI7 · BtGH84 mutant with covalent modification by MA4 in complex with PUGNAc · 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 Q89ZI2
- Elsewhere: RCSB PDB 5MI7 · PDBe 5MI7 · UniProt Q89ZI2
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