MolNFT v1 · #52715 · protein
Structure of a streptococcus pneumoniae family 85 glycoside hydrolase, endo-D, in complex with nag-thiazoline.
2W92 · Endo-beta-N-acetylglucosaminidase D: “Structure of a streptococcus pneumoniae family 85 glycoside hydrolase, endo-D, in complex with nag-thiazoline.”. X-ray diffraction, 1 ligand (NGT), 5 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 2W92
- Type
- protein
- Length
- 635 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase D
- UniProt
- Q93HW0
- Ligands
- NGT
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase D | protein | 635 | 20% helix, 36% strand | Q93HW0 |
Ligands and binding sites
- NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.64 | 0.82 | 44 | empty |
| 2 | 139 | 0.47 | 0.78 | 35 | empty |
| 3 | 99 | 0.42 | 0.77 | 16 | empty |
| 4 | 73 | 0.30 | 0.73 | 16 | empty |
| 5 | 56 | 0.29 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2W92 · Structure of a Streptococcus pneumoniae family 85 glycoside hydrolase, Endo-D, in complex… · 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 Q93HW0
- Elsewhere: RCSB PDB 2W92 · PDBe 2W92 · UniProt Q93HW0
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