MolNFT v1 · #120396 · protein
Structure of D-amino acid dehydrogenase in complex with NADPH and 2- keto-6-aminocapronic acid
5GZ6 · Meso-diaminopimelate D-dehydrogenase: “Structure of D-amino acid dehydrogenase in complex with NADPH and 2- keto-6-aminocapronic acid”. X-ray diffraction, 3 ligands (NDP, 7C3, SO4), 9 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5GZ6
- Type
- protein
- Length
- 634 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
- G1UII1
- Ligands
- NDP, 7C3, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 318 | 41% helix, 27% strand | G1UII1 |
| B | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 316 | 41% helix, 26% strand | G1UII1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 7C3 · 6-azanyl-2-oxidanylidene-hexanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.69 | 0.76 | 59 | NDP, 7C3, SO4 |
| 2 | 371 | 0.58 | 0.75 | 31 | empty |
| 3 | 102 | 0.43 | 0.77 | 19 | empty |
| 4 | 62 | 0.36 | 0.78 | 19 | empty |
| 5 | 112 | 0.35 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2609 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5GZ6 · Structure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic… · the same entry in another collection · chain A against A, TM-score 1.00
- G1UII1 · AlphaFold monomer V2.0 prediction for meso-diaminopimelate D-dehydrogenase (G1UII1) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 G1UII1
- Elsewhere: RCSB PDB 5GZ6 · PDBe 5GZ6 · UniProt G1UII1
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