MolNFT v1 · #113137 · protein
GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with pugnac
5A6B · N-acetyl-beta-D-glucosaminidase: “GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with pugnac”. X-ray diffraction, 2 ligands (OAN, MG), 12 pockets (best druggability 0.76). MolNFT v1 #113137 on GenesisL1: 3D…
- PDB
- 5A6B
- Type
- protein
- Length
- 2,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-beta-D-glucosaminidase
- UniProt
- C1CH75
- Ligands
- OAN, MG
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-beta-D-glucosaminidase | protein | 612 | 49% helix, 13% strand | C1CH75 |
| B | N-acetyl-beta-D-glucosaminidase | protein | 617 | 49% helix, 13% strand | C1CH75 |
| C | N-acetyl-beta-D-glucosaminidase | protein | 610 | 49% helix, 13% strand | C1CH75 |
| D | N-acetyl-beta-D-glucosaminidase | protein | 616 | 50% helix, 13% strand | C1CH75 |
Ligands and binding sites
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.76 | 0.79 | 102 | OAN |
| 2 | 750 | 0.73 | 0.79 | 93 | OAN |
| 3 | 817 | 0.72 | 0.77 | 58 | empty |
| 4 | 323 | 0.59 | 0.77 | 55 | empty |
| 5 | 110 | 0.56 | 0.84 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3322 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3272 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5A6B · GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with PUGNAc · 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 C1CH75
- Elsewhere: RCSB PDB 5A6B · PDBe 5A6B · UniProt C1CH75
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