MolNFT v1 · #114109 · protein
N,N'-diacetylchitobiose deacetylase from pyrococcus horikoshii complexed with its inhibitor mpg (acetate-containing condition)
5B2E · Putative uncharacterized protein PH0499: “N,N'-diacetylchitobiose deacetylase from pyrococcus horikoshii complexed with its inhibitor mpg…”. X-ray diffraction, 2 ligands (MQG, ZN), 8 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5B2E
- Type
- protein
- Length
- 799 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0499
- UniProt
- O58235
- Ligands
- MQG, ZN
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative uncharacterized protein PH0499 | protein | 267 | 43% helix, 15% strand | O58235 |
| B | Putative uncharacterized protein PH0499 | protein | 265 | 45% helix, 15% strand | O58235 |
Ligands and binding sites
- MQG · 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, C, B
- HEZ · Hexane-1,6-diol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.80 | 0.82 | 58 | HEZ |
| 2 | 823 | 0.77 | 0.81 | 58 | MQG, HEZ |
| 3 | 767 | 0.77 | 0.81 | 52 | MQG, HEZ |
| 4 | 774 | 0.77 | 0.81 | 56 | MQG, HEZ |
| 5 | 67 | 0.37 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1868 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1851 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1784 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5B2E · N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its… · 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 O58235
- Elsewhere: RCSB PDB 5B2E · PDBe 5B2E · UniProt O58235
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