MolNFT v1 · #153888 · protein
Crystal structure of nagz from neisseria gonorrhoeae in complex with zinc ion
6JTL · Beta-hexosaminidase: “Crystal structure of nagz from neisseria gonorrhoeae in complex with zinc ion”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.81). MolNFT v1 #153888 on GenesisL1: 3D structure, binding sites…
- 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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