MolNFT v1 · #157860 · protein
Crystal structure of GH2 beta-galacturonidase from eisenbergiella tayi bound to galacturonate
6NCX: “Crystal structure of GH2 beta-galacturonidase from eisenbergiella tayi bound to galacturonate”. X-ray diffraction, 2 ligands (ADA, CL), 20 pockets (best druggability 0.90). MolNFT v1 #157860 on GenesisL1: 3D structure, binding sites…
- PDB
- 6NCX
- Type
- protein
- Length
- 2,227 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galacturonidase
- EC
- 3.2.1.31
- UniProt
- A0A1E3AEY6
- Ligands
- ADA, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Beta-galacturonidase (EC 3.2.1.31) | protein | 555 | 21% helix, 37% strand | A0A1E3AEY6 |
| A | Beta-galacturonidase (EC 3.2.1.31) | protein | 554 | 21% helix, 37% strand | A0A1E3AEY6 |
| B, C | Beta-galacturonidase (EC 3.2.1.31) | protein | 559 | 21% helix, 37% strand | A0A1E3AEY6 |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 4 copies · chains D, A, B, C
- CL · Chloride ion · ion · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.90 | 0.92 | 133 | empty |
| 2 | 904 | 0.82 | 0.84 | 95 | empty |
| 3 | 923 | 0.82 | 0.84 | 92 | empty |
| 4 | 215 | 0.80 | 0.94 | 50 | empty |
| 5 | 201 | 0.80 | 0.94 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1491 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 1488 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 925 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 920 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NCX · Crystal structure of GH2 beta-galacturonidase from Eisenbergiella tayi bound to… · the same entry in another collection · chain D against D, 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 A0A1E3AEY6
- Elsewhere: RCSB PDB 6NCX · PDBe 6NCX · UniProt A0A1E3AEY6
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