MolNFT v1 · #125840 · protein
Structure of the isoleucine 2-epimerase from lactobacillus buchneri (plp complex form)
5LL3: “Structure of the isoleucine 2-epimerase from lactobacillus buchneri (plp complex form)”. X-ray diffraction, 1 ligand (PLP), 12 pockets (best druggability 0.83). MolNFT v1 #125840 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5LL3
- Type
- protein
- Length
- 1,668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoleucine 2-epimerase
- EC
- 5.1.1.21
- UniProt
- M1GRN3
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isoleucine 2-epimerase (EC 5.1.1.21) | protein | 417 | 41% helix, 19% strand | M1GRN3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.83 | 0.96 | 46 | empty |
| 2 | 233 | 0.83 | 0.95 | 47 | empty |
| 3 | 964 | 0.80 | 0.82 | 118 | PLP |
| 4 | 941 | 0.80 | 0.82 | 103 | PLP |
| 5 | 681 | 0.75 | 0.81 | 77 | PLP |
Interfaces
6 interfaces between chains.
- C–D · 3620 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3616 Ų buried · 56 hydrogen bonds · protein-protein
- A–D · 1302 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1298 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LL3 · Structure of the Isoleucine 2-epimerase from Lactobacillus buchneri (PLP complex form) · the same entry in another collection · chain A against A, TM-score 1.00
- M1GRN3 · AlphaFold monomer V2.0 prediction for isoleucine 2-epimerase (M1GRN3) · a predicted model of the same protein · chain A 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 M1GRN3
- Elsewhere: RCSB PDB 5LL3 · PDBe 5LL3 · UniProt M1GRN3
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