MolNFT v1 · #157859 · protein
Crystal structure of a GH2 beta-galacturonidase from eisenbergiella tayi bound to glycerol
6NCW: “Crystal structure of a GH2 beta-galacturonidase from eisenbergiella tayi bound to glycerol”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.87). MolNFT v1 #157859 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NCW
- Type
- protein
- Length
- 2,240 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
- CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galacturonidase (EC 3.2.1.31) | protein | 561 | 21% helix, 37% strand | A0A1E3AEY6 |
| B | Beta-galacturonidase (EC 3.2.1.31) | protein | 560 | 21% helix, 38% strand | A0A1E3AEY6 |
| C | Beta-galacturonidase (EC 3.2.1.31) | protein | 559 | 21% helix, 37% strand | A0A1E3AEY6 |
| D | Beta-galacturonidase (EC 3.2.1.31) | protein | 560 | 21% helix, 37% strand | A0A1E3AEY6 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 10 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.87 | 0.93 | 62 | empty |
| 2 | 1062 | 0.83 | 0.84 | 111 | empty |
| 3 | 1103 | 0.82 | 0.83 | 114 | empty |
| 4 | 206 | 0.81 | 0.95 | 44 | empty |
| 5 | 207 | 0.80 | 0.94 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1485 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1472 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 910 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 903 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 328 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6NCW · Crystal structure of a GH2 beta-galacturonidase from Eisenbergiella tayi bound to glycerol · the same entry in another collection · chain B against B, 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 6NCW · PDBe 6NCW · UniProt A0A1E3AEY6
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