MolNFT v1 · #6028 · protein
Three dimensional structure of the ternary complex of corynebacterium glutamicum diaminopimelate dehydrogenase NADPH-L-2-amino-6-methylene- pimelate
1F06 · Meso-diaminopimelate D-dehydrogenase: “Three dimensional structure of the ternary complex of corynebacterium glutamicum diaminopimelate…”. X-ray diffraction, 2 ligands (NDP, 2NP), 3 pockets (best druggability 0.76). MolNFT v1 #6028…
- PDB
- 1F06
- Type
- protein
- Length
- 640 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
- Ligands
- NDP, 2NP
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 320 | 41% helix, 26% strand | P04964 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 2NP · L-2-amino-6-methylene-pimelic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.76 | 0.82 | 63 | NDP, 2NP |
| 2 | 360 | 0.57 | 0.75 | 36 | NDP |
| 3 | 154 | 0.44 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2728 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1F06 · Three dimensional structure of the ternary complex of corynebacterium glutamicum… · 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 A against A, TM-score 0.92
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 1F06 · PDBe 1F06 · UniProt P04964
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