Research workbench
Structure of dipeptide epimerase from bacteroides thetaiotaomicron complexed with L-ala-D-glu; nonproductive substrate binding.
Analyse Structure of dipeptide epimerase from bacteroides thetaiotaomicron complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJI
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconate cycloisomerase
- UniProt
- Q8A861
- Ligands
- MG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Muconate cycloisomerase | protein | 338 | 38% helix, 23% strand | Q8A861 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.85 | 0.86 | 88 | empty |
| 2 | 142 | 0.48 | 0.78 | 29 | empty |
| 3 | 80 | 0.47 | 0.82 | 22 | empty |
| 4 | 55 | 0.47 | 0.85 | 13 | empty |
| 5 | 56 | 0.43 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 874 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
Compared structures
- 3IJI · Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8A861 · AlphaFold monomer V2.0 prediction for L-ala-D/L-glu epimerase (Q8A861) · 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 Q8A861
- Elsewhere: RCSB PDB 3IJI · PDBe 3IJI · UniProt Q8A861
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