MolNFT v1 · #119685 · protein
Crystal structure of nagz from pseudomonas aeruginosa in complex with N-acetylglucosamine and L-ala-1,6-anhydromurnac
5G3R: “Crystal structure of nagz from pseudomonas aeruginosa in complex with N-acetylglucosamine and…”. X-ray diffraction, 2 ligands (89A, NAG), 6 pockets (best druggability 0.67). MolNFT v1 #119685 on GenesisL1: 3D structure, binding…
- PDB
- 5G3R
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- EC
- 3.2.1.52
- UniProt
- Q9HZK0
- Ligands
- 89A, NAG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (EC 3.2.1.52) | protein | 335 | 41% helix, 13% strand | Q9HZK0 |
| B | (EC 3.2.1.52) | protein | 333 | 41% helix, 15% strand | Q9HZK0 |
Ligands and binding sites
- 89A · 2-[[(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoyl]amino]propanamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.67 | 0.77 | 51 | PEG |
| 2 | 319 | 0.66 | 0.81 | 35 | NAG, 89A |
| 3 | 310 | 0.64 | 0.80 | 29 | NAG, 89A |
| 4 | 192 | 0.50 | 0.76 | 22 | empty |
| 5 | 54 | 0.32 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5G3R · Crystal structure of NagZ from Pseudomonas aeruginosa in complex with N-acetylglucosamine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZK0 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (Q9HZK0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9HZK0
- Elsewhere: RCSB PDB 5G3R · PDBe 5G3R · UniProt Q9HZK0
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