MolNFT v1 · #127210 · protein
Bulgecin a: the key to a broad-spectrum inhibitor that targets lytic transglycosylases
5MPQ: “Bulgecin a: the key to a broad-spectrum inhibitor that targets lytic transglycosylases”. X-ray diffraction, 2 ligands (BLG, MG), 4 pockets (best druggability 0.53). MolNFT v1 #127210 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MPQ
- Type
- protein
- Length
- 576 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transglycosylase
- EC
- 4.2.2.-
- UniProt
- A0A0Y5YPU4
- Ligands
- BLG, MG
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transglycosylase (EC 4.2.2.-) | protein | 576 | 66% helix, 1% strand | A0A0Y5YPU4 |
Ligands and binding sites
- BLG · 4-O-(4-O-sulfonyl-N-acetylglucosamininyl)-5-methylhydroxy-L-proline-taurine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.53 | 0.74 | 48 | BLG, MG |
| 2 | 119 | 0.43 | 0.77 | 18 | empty |
| 3 | 106 | 0.41 | 0.77 | 16 | empty |
| 4 | 136 | 0.41 | 0.75 | 27 | NHE |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MPQ · Bulgecin A: The key to a broad-spectrum inhibitor that targets lytic transglycosylases · 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 A0A0Y5YPU4
- Elsewhere: RCSB PDB 5MPQ · PDBe 5MPQ · UniProt A0A0Y5YPU4
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