MolNFT v1 · #114170 · protein
Crystal structure of lpxh with lipid X in spacegroup P21
5B4A · Udp-2,3-diacylglucosamine hydrolase: “Crystal structure of lpxh with lipid X in spacegroup P21”. X-ray diffraction, 1 ligand (LP5), 6 pockets (best druggability 0.75). MolNFT v1 #114170 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B4A
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-2,3-diacylglucosamine hydrolase
- EC
- 3.6.1.54
- UniProt
- Q9I2V0
- Ligands
- LP5
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54) | protein | 240 | 38% helix, 25% strand | Q9I2V0 |
| B | Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54) | protein | 247 | 38% helix, 26% strand | Q9I2V0 |
Ligands and binding sites
- LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.75 | 0.86 | 46 | LP5, GOL |
| 2 | 330 | 0.73 | 0.85 | 41 | LP5 |
| 3 | 429 | 0.71 | 0.82 | 49 | empty |
| 4 | 357 | 0.66 | 0.80 | 44 | empty |
| 5 | 101 | 0.40 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5B4A · Crystal structure of LpxH with lipid X in spacegroup P21 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I2V0 · AlphaFold monomer V2.0 prediction for udp-2,3-diacylglucosamine hydrolase (Q9I2V0) · 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 Q9I2V0
- Elsewhere: RCSB PDB 5B4A · PDBe 5B4A · UniProt Q9I2V0
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