MolNFT v1 · #120393 · protein
Structure of D-amino acid dehydrogenase in complex with NADP
5GZ3 · Meso-diaminopimelate D-dehydrogenase: “Structure of D-amino acid dehydrogenase in complex with NADP”. X-ray diffraction, 1 ligand (NAP), 5 pockets (best druggability 0.60). MolNFT v1 #120393 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GZ3
- Type
- protein
- Length
- 644 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
- NAP
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 325 | 40% helix, 27% strand | G1UII1 |
| B | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 319 | 41% helix, 28% strand | G1UII1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.60 | 0.76 | 43 | NAP |
| 2 | 424 | 0.59 | 0.75 | 40 | NAP, EDO |
| 3 | 191 | 0.46 | 0.75 | 34 | empty |
| 4 | 110 | 0.37 | 0.74 | 19 | empty |
| 5 | 78 | 0.34 | 0.75 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 3052 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5GZ3 · Structure of D-amino acid dehydrogenase in complex with NADP · 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 B against A, TM-score 0.99
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 5GZ3 · PDBe 5GZ3 · UniProt G1UII1
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