Research workbench
Structure of L-amino acid oxidase from calloselasma rhodostoma in complex with L-phenylalanine
Analyse Structure of L-amino acid oxidase from calloselasma rhodostoma 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
- 2IID
- 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
- UniProt
- P81382
- Ligands
- PHE, FAD, NAG, FUC
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 41% helix, 22% strand | P81382 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, D, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.88 | 0.90 | 132 | PHE, FAD |
| 2 | 1167 | 0.87 | 0.88 | 139 | PHE, FAD |
| 3 | 899 | 0.87 | 0.88 | 104 | PHE, FAD |
| 4 | 862 | 0.86 | 0.88 | 100 | PHE, FAD |
| 5 | 710 | 0.74 | 0.80 | 71 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2097 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2048 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 647 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 644 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2IID · Structure of L-amino acid oxidase from Calloselasma rhodostoma in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- P81382 · AlphaFold monomer V2.0 prediction for L-amino-acid oxidase (P81382) · 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 P81382
- Elsewhere: RCSB PDB 2IID · PDBe 2IID · UniProt P81382
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