Research workbench
Crystal structure of amino transferase (RER070207001803) from eubacterium rectale at 2.10 a resolution
Analyse Crystal structure of amino transferase (RER070207001803) from eubacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ELE
- Type
- protein
- Length
- 1,591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino transferase
- Ligands
- PLP, CL
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Amino transferase | protein | 398 | 45% helix, 14% strand | — |
| C | Amino transferase | protein | 397 | 45% helix, 14% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.78 | 0.84 | 57 | PLP |
| 2 | 636 | 0.77 | 0.82 | 61 | PLP, EDO |
| 3 | 612 | 0.75 | 0.82 | 46 | PLP |
| 4 | 734 | 0.74 | 0.80 | 63 | PLP |
| 5 | 383 | 0.58 | 0.76 | 49 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 2907 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2906 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 86 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3ELE · Crystal structure of Amino Transferase (RER070207001803) from Eubacterium rectale at 2.10… · 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 3ELE · PDBe 3ELE
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