Research workbench
Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with dap 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
- 3WGQ
- 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
- API
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 323 | 37% helix, 27% strand | Q890V3 |
| B | Meso-diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 324 | 38% helix, 27% strand | Q890V3 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · chains A, 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 | 549 | 0.68 | 0.78 | 57 | empty |
| 2 | 349 | 0.61 | 0.78 | 50 | empty |
| 3 | 203 | 0.45 | 0.74 | 42 | empty |
| 4 | 76 | 0.40 | 0.79 | 19 | empty |
| 5 | 110 | 0.38 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3024 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3WGQ · Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with DAP of… · 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 3WGQ · PDBe 3WGQ · UniProt Q890V3
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