MolNFT v1 · #129468 · protein
Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from zobellia galactanivorans
5OLC · Galactonate dehydratase: “Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from zobellia galactanivorans”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.82). MolNFT v1 #129468 on GenesisL1: 3D…
- PDB
- 5OLC
- Type
- protein
- Length
- 2,808 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactonate dehydratase
- EC
- 4.2.1.6
- UniProt
- G0L7B8
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Galactonate dehydratase (EC 4.2.1.6) | protein | 351 | 45% helix, 22% strand | G0L7B8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.97 | 30 | empty |
| 2 | 164 | 0.82 | 0.97 | 32 | empty |
| 3 | 174 | 0.82 | 0.96 | 32 | empty |
| 4 | 166 | 0.81 | 0.96 | 32 | empty |
| 5 | 518 | 0.79 | 0.86 | 66 | empty |
Interfaces
16 interfaces between chains.
- B–H · 1383 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1368 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1365 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1360 Ų buried · 20 hydrogen bonds · protein-protein
- D–G · 1206 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5OLC · Crystal structure of the 3,6-anhydro-D-galactonate cycloisomerase from Zobellia… · 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 G0L7B8
- Elsewhere: RCSB PDB 5OLC · PDBe 5OLC · UniProt G0L7B8
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