Research workbench
Crystal structure of the Y766F mutant of goxa soaked with glycine
Analyse Crystal structure of the Y766F mutant of goxa soaked with glycine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VMF
- Type
- protein
- Length
- 3,075 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine oxidase
- UniProt
- A0A161XU12
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine oxidase | protein | 754 | 30% helix, 21% strand | A0A161XU12 |
| B | Glycine oxidase | protein | 773 | 32% helix, 20% strand | A0A161XU12 |
| C | Glycine oxidase | protein | 770 | 32% helix, 21% strand | A0A161XU12 |
| D | Glycine oxidase | protein | 778 | 34% helix, 20% strand | A0A161XU12 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.86 | 0.93 | 55 | empty |
| 2 | 452 | 0.84 | 0.92 | 55 | empty |
| 3 | 1121 | 0.80 | 0.82 | 109 | empty |
| 4 | 1005 | 0.80 | 0.82 | 109 | empty |
| 5 | 124 | 0.76 | 0.95 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3090 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 3061 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 2255 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2073 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6VMF · Crystal structure of the Y766F mutant of GoxA soaked with glycine · 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 A0A161XU12
- Elsewhere: RCSB PDB 6VMF · PDBe 6VMF · UniProt A0A161XU12
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