Research workbench
Crystal structure of the F316A mutant of goxa soaked with glycine
Analyse Crystal structure of the F316A 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
- 6VMW
- Type
- protein
- Length
- 3,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine oxidase
- UniProt
- A0A161XU12
- Ligands
- MG, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glycine oxidase | protein | 784 | 32% helix, 20% strand | A0A161XU12 |
| A | Glycine oxidase | protein | 764 | 31% helix, 21% strand | A0A161XU12 |
| C | Glycine oxidase | protein | 769 | 32% helix, 21% strand | A0A161XU12 |
| D | Glycine oxidase | protein | 759 | 32% helix, 21% strand | A0A161XU12 |
Ligands and binding sites
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 | 642 | 0.88 | 0.92 | 77 | empty |
| 2 | 482 | 0.86 | 0.93 | 55 | empty |
| 3 | 914 | 0.80 | 0.83 | 101 | empty |
| 4 | 571 | 0.78 | 0.85 | 80 | empty |
| 5 | 147 | 0.76 | 0.94 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3142 Ų buried · 63 hydrogen bonds · protein-protein
- B–A · 3083 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 2510 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2474 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 236 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6VMW · Crystal structure of the F316A mutant of GoxA soaked with glycine · 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 A0A161XU12
- Elsewhere: RCSB PDB 6VMW · PDBe 6VMW · UniProt A0A161XU12
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