Research workbench
Crystal structure of nagz from neisseria gonorrhoeae in complex with N-trifluoroacetyl-D-glucosamine
Analyse Crystal structure of nagz from neisseria gonorrhoeae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JTK
- Type
- protein
- Length
- 2,042 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q5FA94
- Ligands
- C76
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 334 | 45% helix, 14% strand | Q5FA94 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 346 | 45% helix, 14% strand | Q5FA94 |
| C | Beta-hexosaminidase (EC 3.2.1.52) | protein | 339 | 44% helix, 13% strand | Q5FA94 |
| D | Beta-hexosaminidase (EC 3.2.1.52) | protein | 344 | 44% helix, 13% strand | Q5FA94 |
| E | Beta-hexosaminidase (EC 3.2.1.52) | protein | 339 | 45% helix, 13% strand | Q5FA94 |
| F | Beta-hexosaminidase (EC 3.2.1.52) | protein | 340 | 44% helix, 13% strand | Q5FA94 |
Ligands and binding sites
- C76 · 2,2,2-tris(fluoranyl)-N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide · ligand · 4 copies · chains A, C, B, F, D, E
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 | 1180 | 0.84 | 0.85 | 106 | C76 |
| 2 | 1007 | 0.82 | 0.83 | 89 | C76 |
| 3 | 446 | 0.77 | 0.86 | 43 | C76 |
| 4 | 102 | 0.77 | 0.97 | 25 | empty |
| 5 | 719 | 0.68 | 0.76 | 62 | empty |
Interfaces
7 interfaces between chains.
- B–F · 1425 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1420 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 241 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6JTK · Crystal structure of NagZ from Neisseria gonorrhoeae in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q5FA94 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q5FA94) · 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 Q5FA94
- Elsewhere: RCSB PDB 6JTK · PDBe 6JTK · UniProt Q5FA94
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