Research workbench
Crystal structure of the H583C mutant of goxa soaked with glycine
Analyse Crystal structure of the H583C 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
- 6VL7
- Type
- protein
- Length
- 3,105 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 0.88
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine oxidase | protein | 777 | 32% helix, 20% strand | A0A161XU12 |
| B | Glycine oxidase | protein | 782 | 32% helix, 20% strand | A0A161XU12 |
| C | Glycine oxidase | protein | 774 | 32% helix, 21% strand | A0A161XU12 |
| D | Glycine oxidase | protein | 772 | 32% helix, 21% strand | A0A161XU12 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · 3 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 629 | 0.88 | 0.92 | 71 | empty |
| 2 | 491 | 0.85 | 0.91 | 54 | empty |
| 3 | 574 | 0.79 | 0.85 | 84 | empty |
| 4 | 538 | 0.78 | 0.85 | 78 | empty |
| 5 | 150 | 0.76 | 0.93 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3075 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 3037 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2168 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2147 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6VL7 · Crystal structure of the H583C 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 6VL7 · PDBe 6VL7 · UniProt A0A161XU12
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