Research workbench
Crystal structure of zn bound cbsa from thermotoga neapolitana
Analyse Crystal structure of zn bound cbsa from thermotoga neapolitana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C0Q
- Type
- protein
- Length
- 1,782 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
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 450 | 43% helix, 16% strand | Q9AG27 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 457 | 43% helix, 15% strand | Q9AG27 |
| C | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 441 | 42% helix, 14% strand | Q9AG27 |
| D | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 434 | 45% helix, 14% strand | Q9AG27 |
Ligands and binding sites
- ZN · Zinc ion · metal · 35 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.79 | 0.86 | 80 | empty |
| 2 | 413 | 0.78 | 0.87 | 68 | empty |
| 3 | 494 | 0.66 | 0.78 | 46 | ZN |
| 4 | 266 | 0.65 | 0.82 | 37 | ZN |
| 5 | 328 | 0.62 | 0.79 | 37 | ZN |
Interfaces
6 interfaces between chains.
- A–B · 2645 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2484 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 568 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 111 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5C0Q · Crystal structure of Zn bound 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 5C0Q · PDBe 5C0Q · UniProt Q9AG27
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