MolNFT v1 · #79007 · protein
Crystal structure of glycoside hydrolase from synechococcus complexed with N-acetyl-D-glucosamine
3SQM · Glycosyl hydrolase family 3: “Crystal structure of glycoside hydrolase from synechococcus complexed with N-acetyl-D-glucosamine”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best druggability 0.87). MolNFT v1 #79007 on…
- PDB
- 3SQM
- Type
- protein
- Length
- 2,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 3
- UniProt
- B1XLD2
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 3 | protein | 514 | 42% helix, 14% strand | B1XLD2 |
| B | Glycosyl hydrolase family 3 | protein | 516 | 42% helix, 14% strand | B1XLD2 |
| C | Glycosyl hydrolase family 3 | protein | 519 | 43% helix, 14% strand | B1XLD2 |
| D | Glycosyl hydrolase family 3 | protein | 519 | 40% helix, 14% strand | B1XLD2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- ACY · Acetic acid · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.87 | 0.90 | 107 | empty |
| 2 | 846 | 0.87 | 0.90 | 102 | GOL |
| 3 | 82 | 0.76 | 0.98 | 28 | NAG |
| 4 | 79 | 0.76 | 0.98 | 23 | NAG |
| 5 | 1064 | 0.76 | 0.78 | 107 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2933 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2904 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 3SQM · Crystal Structure of Glycoside Hydrolase from Synechococcus Complexed with… · 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 B1XLD2
- Elsewhere: RCSB PDB 3SQM · PDBe 3SQM · UniProt B1XLD2
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