MolNFT v1 · #116889 · protein
Structure of the AALPXC/LPC-023 complex
5DRP · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Structure of the AALPXC/LPC-023 complex”. X-ray diffraction, 3 ligands (5EP, ZN, CL), 4 pockets (best druggability 0.83). MolNFT v1 #116889 on GenesisL1: 3D structure…
- PDB
- 5DRP
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- 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
- O67648
- Ligands
- 5EP, ZN, CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 267 | 24% helix, 34% strand | O67648 |
Ligands and binding sites
- 5EP · N~2~-{4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]benzoyl}-N-hydroxy-L-isoleucinamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.83 | 0.84 | 106 | 5EP |
| 2 | 502 | 0.73 | 0.82 | 43 | 5EP, CL, DMS |
| 3 | 75 | 0.40 | 0.79 | 20 | empty |
| 4 | 53 | 0.35 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 13 hydrogen bonds · protein-protein
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 O67648
- Elsewhere: RCSB PDB 5DRP · PDBe 5DRP · UniProt O67648
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