MolNFT v1 · #16329 · protein
Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
1NVM · 4-hydroxy-2-oxovalerate aldolase: “Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate”. X-ray diffraction, 4 ligands (OXL, NAD, MN), 20 pockets (best druggability 0.76).…
- PDB
- 1NVM
- Type
- protein
- Length
- 2,590 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxovalerate aldolase; Acetaldehyde dehydrogenase (acylating)
- EC
- 4.1.3.-, 1.2.1.10
- UniProt
- P51016, Q52060
- Ligands
- OXL, NAD, MN, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.-) | protein | 340 | 49% helix, 15% strand | P51016 |
| B | Acetaldehyde dehydrogenase (acylating) (EC 1.2.1.10) | protein | 312 | 40% helix, 26% strand | Q52060 |
| C | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.-) | protein | 337 | 49% helix, 15% strand | P51016 |
| D | Acetaldehyde dehydrogenase (acylating) (EC 1.2.1.10) | protein | 308 | 40% helix, 27% strand | Q52060 |
| E | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.-) | protein | 338 | 48% helix, 15% strand | P51016 |
| F | Acetaldehyde dehydrogenase (acylating) (EC 1.2.1.10) | protein | 309 | 40% helix, 27% strand | Q52060 |
| G | 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.-) | protein | 339 | 48% helix, 16% strand | P51016 |
| H | Acetaldehyde dehydrogenase (acylating) (EC 1.2.1.10) | protein | 307 | 40% helix, 26% strand | Q52060 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 4 copies · chains A, C, E, G
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, D, H
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, E, G, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, C, B, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.76 | 0.92 | 32 | empty |
| 2 | 72 | 0.76 | 0.99 | 17 | empty |
| 3 | 169 | 0.76 | 0.92 | 32 | empty |
| 4 | 70 | 0.76 | 0.99 | 19 | empty |
| 5 | 61 | 0.74 | 0.99 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1657 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1597 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1569 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1525 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1NVM · Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and… · the same entry in another collection · chain H against H, TM-score 1.00
- P51016 · AlphaFold monomer V2.0 prediction for 4-hydroxy-2-oxovalerate aldolase (P51016) · a predicted model of the same protein · chain E 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 P51016
- Every structure of UniProt Q52060
- Elsewhere: RCSB PDB 1NVM · PDBe 1NVM · UniProt P51016 · UniProt Q52060
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