Research workbench
Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with D-leucine of from clostridium tetani E88
Analyse Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WGZ
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meso-diaminopimelate dehydrogenase
- EC
- 1.4.1.16
- UniProt
- Q890V3
- Ligands
- DLE
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 323 | 37% helix, 25% strand | Q890V3 |
| B | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 324 | 38% helix, 26% strand | Q890V3 |
Ligands and binding sites
- DLE · D-leucine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.69 | 0.78 | 55 | empty |
| 2 | 452 | 0.64 | 0.77 | 58 | empty |
| 3 | 179 | 0.45 | 0.75 | 32 | empty |
| 4 | 57 | 0.40 | 0.81 | 20 | empty |
| 5 | 113 | 0.39 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3000 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 3WGZ · Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with D-leucine… · 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 Q890V3
- Elsewhere: RCSB PDB 3WGZ · PDBe 3WGZ · UniProt Q890V3
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