Research workbench
Crystal structure of L-amino acid oxidase from calloselasma rhodostoma complexed with citrate
Analyse Crystal structure of L-amino acid oxidase from calloselasma rhodostoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F8R
- Type
- protein
- Length
- 1,932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid oxidase
- EC
- 1.4.3.2
- Ligands
- FAD, NAG, FUC
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-amino acid oxidase (EC 1.4.3.2) | protein | 483 | 40% helix, 22% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.89 | 0.91 | 115 | CIT, FAD |
| 2 | 807 | 0.88 | 0.91 | 117 | CIT, FAD |
| 3 | 1183 | 0.88 | 0.89 | 148 | CIT, FAD |
| 4 | 781 | 0.88 | 0.91 | 107 | CIT, FAD |
| 5 | 58 | 0.75 | 1.00 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2052 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2040 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 649 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 38 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 1F8R · Crystal structure of L-amino acid oxidase from calloselasma rhodostoma complexed with… · 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
- Elsewhere: RCSB PDB 1F8R · PDBe 1F8R
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