Research workbench
The structure of a substrate-liganded complex of the L-ala- D/L-glu epimerase from bacillus subtilis
Analyse The structure of a substrate-liganded complex of the L-ala- D/L-glu epimerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TKK
- Type
- protein
- Length
- 2,886 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to chloromuconate cycloisomerase
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Similar to chloromuconate cycloisomerase | protein | 361 | 41% helix, 25% strand | — |
| B, F | Similar to chloromuconate cycloisomerase | protein | 360 | 40% helix, 25% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.84 | 0.92 | 56 | empty |
| 2 | 395 | 0.84 | 0.92 | 56 | empty |
| 3 | 381 | 0.83 | 0.92 | 52 | empty |
| 4 | 328 | 0.83 | 0.93 | 48 | empty |
| 5 | 308 | 0.78 | 0.89 | 39 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1391 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1354 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1328 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 728 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1TKK · The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from… · 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 1TKK · PDBe 1TKK
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