Research workbench
The three dimensional structure of diaminopimelate decarboxylase from mycobacterium tuberculosis reveals a tetrameric enzyme organisation
Analyse The three dimensional structure of diaminopimelate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O0T
- Type
- protein
- Length
- 1,784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- P0A5M4
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 446 | 33% helix, 28% strand | P0A5M4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.71 | 0.81 | 69 | SO4 |
| 2 | 468 | 0.70 | 0.80 | 64 | SO4 |
| 3 | 463 | 0.67 | 0.79 | 53 | empty |
| 4 | 424 | 0.65 | 0.78 | 49 | empty |
| 5 | 505 | 0.65 | 0.77 | 81 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3701 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 3618 Ų buried · 79 hydrogen bonds · protein-protein
- B–D · 429 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 402 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, cofactor).
Compared structures
- 2O0T · The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium… · 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
- Every structure of UniProt P0A5M4
- Elsewhere: RCSB PDB 2O0T · PDBe 2O0T · UniProt P0A5M4
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