Research workbench
Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate 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
- 3WGY
- 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
- COI
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 323 | 39% helix, 27% strand | Q890V3 |
| B | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 324 | 40% helix, 26% strand | Q890V3 |
Ligands and binding sites
- COI · 2-oxo-4-methylpentanoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.66 | 0.77 | 49 | empty |
| 2 | 457 | 0.64 | 0.77 | 63 | empty |
| 3 | 190 | 0.45 | 0.74 | 39 | empty |
| 4 | 75 | 0.39 | 0.78 | 18 | empty |
| 5 | 99 | 0.34 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3009 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 3WGY · Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with… · the same entry in another collection · chain B against B, 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 3WGY · PDBe 3WGY · UniProt Q890V3
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