Research workbench
Crystal structure of human augmenter of liver regeneration (alr)
Analyse Crystal structure of human augmenter of liver regeneration (alr) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBG
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-linked sulfhydryl oxidase alr
- EC
- 1.8.3.2
- UniProt
- P55789
- Ligands
- FAD, ZN, NA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | FAD-linked sulfhydryl oxidase alr (EC 1.8.3.2) | protein | 112 | 67% helix, 0% strand | P55789 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 10 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- ACT · Acetate ion · additive · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.74 | 0.86 | 42 | FAD |
| 2 | 341 | 0.70 | 0.83 | 52 | FAD, ACT |
| 3 | 305 | 0.70 | 0.83 | 43 | ZN, FAD, ACT |
| 4 | 183 | 0.47 | 0.76 | 27 | empty |
| 5 | 80 | 0.34 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1476 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 513 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3MBG · Crystal Structure of Human Augmenter of Liver Regeneration (ALR) · the same entry in another collection · chain A against A, TM-score 1.00
- P55789 · AlphaFold monomer V2.0 prediction for FAD-linked sulfhydryl oxidase alr (P55789) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P55789
- Elsewhere: RCSB PDB 3MBG · PDBe 3MBG · UniProt P55789
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