Research workbench
Crystal structure of H10N mutant of lpxh with manganese
Analyse Crystal structure of H10N mutant of lpxh with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B4C
- Type
- protein
- Length
- 462 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
- MN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54) | protein | 231 | 37% helix, 26% strand | Q9I2V0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.69 | 0.80 | 46 | GOL |
| 2 | 420 | 0.69 | 0.80 | 46 | GOL |
| 3 | 643 | 0.68 | 0.77 | 46 | empty |
| 4 | 262 | 0.61 | 0.80 | 35 | empty |
| 5 | 88 | 0.40 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5B4C · Crystal structure of H10N mutant of LpxH with manganese · 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 0.98
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 5B4C · PDBe 5B4C · UniProt Q9I2V0
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