MolNFT v1 · #169742 · protein
The 1.23 ångström crystal structure of galactose oxidase variant with genetically incorporated CL2-TYR272
6XLR: “The 1.23 ångström crystal structure of galactose oxidase variant with genetically incorporated CL2-TYR272”. X-ray diffraction, 2 ligands (CU, CA), 5 pockets (best druggability 0.59). MolNFT v1 #169742 on GenesisL1: 3D structure…
- PDB
- 6XLR
- Type
- protein
- Length
- 639 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose oxidase
- EC
- 1.1.3.9
- UniProt
- P0CS93
- Ligands
- CU, CA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactose oxidase (EC 1.1.3.9) | protein | 639 | 4% helix, 42% strand | P0CS93 |
Ligands and binding sites
- CU · Copper (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 12 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.59 | 0.92 | 19 | GOL |
| 2 | 223 | 0.51 | 0.76 | 30 | GOL |
| 3 | 161 | 0.44 | 0.75 | 27 | GOL |
| 4 | 53 | 0.29 | 0.76 | 17 | ACT |
| 5 | 53 | 0.29 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 6XLR · The 1.23 Angstrom crystal structure of galactose oxidase variant with genetically… · the same entry in another collection · chain A against A, TM-score 1.00
- P0CS93 · AlphaFold monomer V2.0 prediction for galactose oxidase (P0CS93) · a predicted model of the same protein · 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 P0CS93
- Elsewhere: RCSB PDB 6XLR · PDBe 6XLR · UniProt P0CS93
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