MolNFT v1 · #114755 · protein
Crystal structure of cbsa from thermotoga neapolitana
5BZA · Beta-N-acetylhexosaminidase: “Crystal structure of cbsa from thermotoga neapolitana”. X-ray diffraction, 1 ligand (CD), 20 pockets (best druggability 0.82). MolNFT v1 #114755 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5BZA
- Type
- protein
- Length
- 1,763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q9AG27
- Ligands
- CD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 447 | 45% helix, 16% strand | Q9AG27 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 450 | 44% helix, 16% strand | Q9AG27 |
| C | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 434 | 44% helix, 13% strand | Q9AG27 |
| D | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 432 | 45% helix, 15% strand | Q9AG27 |
Ligands and binding sites
- CD · Cadmium ion · metal · 33 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.82 | 0.83 | 107 | empty |
| 2 | 444 | 0.77 | 0.85 | 55 | empty |
| 3 | 470 | 0.68 | 0.80 | 59 | CD |
| 4 | 141 | 0.67 | 0.88 | 24 | empty |
| 5 | 435 | 0.64 | 0.77 | 42 | CD |
Interfaces
6 interfaces between chains.
- A–B · 2371 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2321 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 563 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5BZA · Crystal structure of CbsA from Thermotoga neapolitana · 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 Q9AG27
- Elsewhere: RCSB PDB 5BZA · PDBe 5BZA · UniProt Q9AG27
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