Research workbench
Crystal structure of nagz from neisseria gonorrhoeae in complex with zinc ion
Analyse Crystal structure of nagz from neisseria gonorrhoeae in complex with zinc ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JTL
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q5FA94
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 333 | 45% helix, 14% strand | Q5FA94 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 337 | 44% helix, 13% strand | Q5FA94 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.81 | 0.82 | 81 | ZN |
| 2 | 416 | 0.58 | 0.75 | 60 | empty |
| 3 | 84 | 0.33 | 0.74 | 18 | empty |
| 4 | 92 | 0.33 | 0.74 | 21 | empty |
| 5 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 993 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6JTL · Crystal structure of NagZ from Neisseria gonorrhoeae in complex with zinc ion · the same entry in another collection · chain A against A, 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 6JTL · PDBe 6JTL · UniProt Q5FA94
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