Research workbench
Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide
Analyse Crystal structure of dipeptide epimerase from Thermotoga maritima complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DEQ
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Thermotoga maritima MSB8
- Molecule
- Muconate cycloisomerase
- UniProt
- Q9WXM1
- Ligands
- MG
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Muconate cycloisomerase | protein | 343 | 42% helix, 24% strand | Q9WXM1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.82 | 0.90 | 42 | empty |
| 2 | 497 | 0.81 | 0.88 | 50 | empty |
| 3 | 428 | 0.80 | 0.89 | 48 | empty |
| 4 | 153 | 0.71 | 0.90 | 25 | empty |
| 5 | 126 | 0.64 | 0.88 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1365 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1015 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1003 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 511 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3DEQ · Crystal structure of dipeptide epimerase from thermotoga maritima complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WXM1 · AlphaFold monomer V2.0 prediction for L-ala-D/L-glu epimerase (Q9WXM1) · a predicted model of the same protein · chain C 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 Q9WXM1
- Elsewhere: RCSB PDB 3DEQ · PDBe 3DEQ · UniProt Q9WXM1
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