MolNFT v1 · #104048 · protein
Structure of zm ALDH2-6 (RF2F) in complex with NAD
4PZ2 · Zmaldh: “Structure of zm ALDH2-6 (RF2F) in complex with NAD”. X-ray diffraction, 2 ligands (NAD, NA), 16 pockets (best druggability 0.87). MolNFT v1 #104048 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PZ2
- Type
- protein
- Length
- 1,967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zmaldh
- UniProt
- K7VEU7
- Ligands
- NAD, NA
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Zmaldh | protein | 491 | 40% helix, 22% strand | K7VEU7 |
| B | Zmaldh | protein | 494 | 39% helix, 22% strand | K7VEU7 |
| D | Zmaldh | protein | 491 | 40% helix, 22% strand | K7VEU7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.87 | 0.88 | 104 | empty |
| 2 | 1006 | 0.87 | 0.88 | 145 | NAD, EDO |
| 3 | 1173 | 0.85 | 0.86 | 154 | EDO, NAD |
| 4 | 571 | 0.84 | 0.89 | 70 | empty |
| 5 | 108 | 0.78 | 0.97 | 26 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 2585 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2577 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1524 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1492 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1358 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4PZ2 · Structure of Zm ALDH2-6 (RF2F) in complex with NAD · 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 K7VEU7
- Elsewhere: RCSB PDB 4PZ2 · PDBe 4PZ2 · UniProt K7VEU7
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