Research workbench
Crystal structures of meso-diaminopimelate dehydrogenase from symbiobacterium thermophilum
Analyse Crystal structures of meso-diaminopimelate dehydrogenase from symbiobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WBB
- Type
- protein
- Length
- 891 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate dehydrogenase
- EC
- 1.4.1.16
- UniProt
- Q67PI3
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 297 | 36% helix, 32% strand | Q67PI3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 11 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.75 | 0.77 | 93 | GOL, NAP |
| 2 | 784 | 0.70 | 0.76 | 78 | NAP |
| 3 | 534 | 0.68 | 0.78 | 40 | NAP |
| 4 | 278 | 0.58 | 0.78 | 43 | GOL |
| 5 | 79 | 0.34 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2740 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 660 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WBB · Crystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum · 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 Q67PI3
- Elsewhere: RCSB PDB 3WBB · PDBe 3WBB · UniProt Q67PI3
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