Research workbench
Crystal structure of diaminopimelate decarboxylase from M. jannaschi
Analyse Crystal structure of diaminopimelate decarboxylase from M. jannaschi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TUF
- Type
- protein
- Length
- 868 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- Q58497
- Ligands
- AZ1
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 434 | 34% helix, 26% strand | Q58497 |
Ligands and binding sites
- AZ1 · Azelaic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.74 | 0.97 | 23 | empty |
| 2 | 153 | 0.72 | 0.91 | 35 | empty |
| 3 | 238 | 0.63 | 0.82 | 29 | empty |
| 4 | 350 | 0.62 | 0.78 | 44 | AZ1 |
| 5 | 286 | 0.59 | 0.78 | 35 | AZ1 |
Interfaces
1 interface between chains.
- A–B · 4089 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 1TUF · Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi · the same entry in another collection · chain A against A, TM-score 1.00
- Q58497 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (Q58497) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q58497
- Elsewhere: RCSB PDB 1TUF · PDBe 1TUF · UniProt Q58497
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