Research workbench
Structure of lpxc bound to the reaction product udp-(3-O-(R-3- hydroxymyristoyl))-glucosamine
Analyse Structure of lpxc bound to the reaction product udp-(3-O-(R-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MDT
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- K0BGQ2
- Ligands
- 24G, ZN, PO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 300 | 28% helix, 32% strand | K0BGQ2 |
| C | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 299 | 24% helix, 32% strand | K0BGQ2 |
| D | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 293 | 25% helix, 31% strand | K0BGQ2 |
Ligands and binding sites
- 24G · uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.79 | 0.86 | 74 | empty |
| 2 | 365 | 0.75 | 0.86 | 44 | empty |
| 3 | 315 | 0.67 | 0.82 | 41 | 24G, PO4 |
| 4 | 376 | 0.67 | 0.80 | 41 | 24G, PO4 |
| 5 | 392 | 0.67 | 0.80 | 43 | 24G, PO4 |
Interfaces
5 interfaces between chains.
- C–D · 803 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 631 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 609 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4MDT · Structure of LpxC bound to the reaction product… · 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 K0BGQ2
- Elsewhere: RCSB PDB 4MDT · PDBe 4MDT · UniProt K0BGQ2
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