MolNFT v1 · #83218 · protein
Crystal structure of meso-diaminopimelate dehydrogenase from symbiobacterium thermophilum co-crystallized with NADP+ and dap
3WBF: “Crystal structure of meso-diaminopimelate dehydrogenase from symbiobacterium thermophilum co-crystallized…”. X-ray diffraction, 2 ligands (API, NAP), 7 pockets (best druggability 0.76). MolNFT v1 #83218 on GenesisL1: 3D structure…
- PDB
- 3WBF
- 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
- API, NAP
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Diaminopimelate dehydrogenase (EC 1.4.1.16) | protein | 297 | 35% helix, 32% strand | Q67PI3 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · 3 copies · chains A, B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 16 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.76 | 0.80 | 105 | API, GOL, NAP |
| 2 | 523 | 0.73 | 0.82 | 64 | API, NAP |
| 3 | 525 | 0.72 | 0.81 | 65 | API, NAP |
| 4 | 262 | 0.57 | 0.78 | 34 | GOL |
| 5 | 453 | 0.56 | 0.73 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2756 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3WBF · Crystal Structure 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 3WBF · PDBe 3WBF · UniProt Q67PI3
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