Research workbench
Crystal structure of glycine oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate
Analyse Crystal structure of glycine oxidase G51S/A54R/H244A mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IF9
- Type
- protein
- Length
- 1,449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine oxidase
- EC
- 1.4.3.19
- UniProt
- O31616
- Ligands
- GOA, FAD
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine oxidase (EC 1.4.3.19) | protein | 364 | 32% helix, 27% strand | O31616 |
| B | Glycine oxidase (EC 1.4.3.19) | protein | 363 | 33% helix, 27% strand | O31616 |
| C | Glycine oxidase (EC 1.4.3.19) | protein | 361 | 32% helix, 29% strand | O31616 |
| D | Glycine oxidase (EC 1.4.3.19) | protein | 361 | 33% helix, 28% strand | O31616 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.89 | 0.90 | 147 | GOA, FAD |
| 2 | 344 | 0.81 | 0.91 | 57 | GOA, FAD |
| 3 | 619 | 0.79 | 0.84 | 77 | GOA, FAD |
| 4 | 248 | 0.54 | 0.77 | 31 | empty |
| 5 | 180 | 0.52 | 0.78 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 967 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 541 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IF9 · Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor… · the same entry in another collection · chain C against C, TM-score 1.00
- O31616 · AlphaFold monomer V2.0 prediction for glycine oxidase (O31616) · a predicted model of the same protein · chain D 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 O31616
- Elsewhere: RCSB PDB 3IF9 · PDBe 3IF9 · UniProt O31616
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