Research workbench
Crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and 5'-deoxyadenosine
Analyse Crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XRS
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lysine 5,6-aminomutase alpha subunit; D-lysine 5,6-aminomutase beta subunit
- EC
- 5.4.3.3
- UniProt
- Q9ZFE6, Q9ZFE5
- Ligands
- B12, PLP, 5AD
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-lysine 5,6-aminomutase alpha subunit (EC 5.4.3.3) | protein | 516 | 55% helix, 8% strand | Q9ZFE6 |
| B | D-lysine 5,6-aminomutase beta subunit (EC 5.4.3.3) | protein | 212 | 39% helix, 25% strand | Q9ZFE5 |
Ligands and binding sites
- B12 · Cobalamin · ligand · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.77 | 0.81 | 59 | PLP |
| 2 | 205 | 0.65 | 0.84 | 25 | empty |
| 3 | 367 | 0.56 | 0.75 | 56 | empty |
| 4 | 120 | 0.56 | 0.83 | 20 | empty |
| 5 | 203 | 0.49 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 995 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1XRS · Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and… · 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 Q9ZFE6
- Every structure of UniProt Q9ZFE5
- Elsewhere: RCSB PDB 1XRS · PDBe 1XRS · UniProt Q9ZFE6 · UniProt Q9ZFE5
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