MolNFT v1 · #30651 · protein
2.1 ångström X-ray crystal structure of lysine-2,3-aminomutase from clostridium subterminale SB4, with michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).
2A5H · L-lysine 2,3-aminomutase: “2.1 ångström X-ray crystal structure of lysine-2,3-aminomutase from clostridium subterminale SB4, with…”. X-ray diffraction, 6 ligands (SAM, LYS, PLP), 20 pockets (best druggability 0.87). MolNFT v1 #30651…
- PDB
- 2A5H
- Type
- protein
- Length
- 1,638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine 2,3-aminomutase
- EC
- 5.4.3.2
- Ligands
- SAM, LYS, PLP, SF4, ZN, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lysine 2,3-aminomutase (EC 5.4.3.2) | protein | 409 | 33% helix, 18% strand | — |
| B, D | L-lysine 2,3-aminomutase (EC 5.4.3.2) | protein | 410 | 32% helix, 18% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.87 | 0.88 | 132 | empty |
| 2 | 416 | 0.86 | 0.94 | 49 | SAM, LYS, PLP, SF4 |
| 3 | 410 | 0.86 | 0.94 | 49 | SAM, LYS, PLP, SF4 |
| 4 | 417 | 0.86 | 0.94 | 47 | SAM, LYS, PLP, SF4 |
| 5 | 407 | 0.86 | 0.94 | 46 | SAM, LYS, PLP, SF4 |
Interfaces
6 interfaces between chains.
- A–B · 4548 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 4518 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 1510 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1506 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1221 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2A5H · 2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium… · 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 2A5H · PDBe 2A5H
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