MolNFT v1 · #139354 · protein
Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase
5XD8 · 3,6-anhydro-alpha-L-galactonate cycloisomerase: “Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.70). MolNFT v1 #139354 on GenesisL1: 3D…
- PDB
- 5XD8
- Type
- protein
- Length
- 719 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,6-anhydro-alpha-L-galactonate cycloisomerase
- EC
- 5.5.1.25
- UniProt
- H2IFX0
- Ligands
- MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,6-anhydro-alpha-L-galactonate cycloisomerase (EC 5.5.1.25) | protein | 352 | 42% helix, 22% strand | H2IFX0 |
| B | 3,6-anhydro-alpha-L-galactonate cycloisomerase (EC 5.5.1.25) | protein | 367 | 42% helix, 20% strand | H2IFX0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.70 | 0.95 | 26 | empty |
| 2 | 452 | 0.65 | 0.78 | 54 | empty |
| 3 | 52 | 0.64 | 0.94 | 20 | empty |
| 4 | 65 | 0.61 | 0.91 | 24 | empty |
| 5 | 221 | 0.53 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2072 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5XD8 · Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase · the same entry in another collection · chain A against A, TM-score 1.00
- H2IFX0 · AlphaFold monomer V2.0 prediction for 3,6-anhydro-alpha-L-galactonate cycloisomerase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 H2IFX0
- Elsewhere: RCSB PDB 5XD8 · PDBe 5XD8 · UniProt H2IFX0
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