Research workbench
Crystal structure of the engineered D-amino acid dehydrogenase (daadh)
Analyse Crystal structure of the engineered D-amino acid dehydrogenase (daadh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LOC
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meso-diaminopimelate D-dehydrogenase
- EC
- 1.4.1.16
- UniProt
- P04964
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 320 | 40% helix, 25% strand | P04964 |
| B | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 317 | 37% helix, 26% strand | P04964 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.71 | 0.78 | 77 | empty |
| 2 | 603 | 0.68 | 0.77 | 53 | empty |
| 3 | 224 | 0.53 | 0.76 | 23 | empty |
| 4 | 59 | 0.33 | 0.77 | 14 | empty |
| 5 | 50 | 0.29 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2745 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5LOC · Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) · the same entry in another collection · chain A against A, TM-score 1.00
- P04964 · AlphaFold monomer V2.0 prediction for meso-diaminopimelate D-dehydrogenase (P04964) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P04964
- Elsewhere: RCSB PDB 5LOC · PDBe 5LOC · UniProt P04964
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