Research workbench
1.94 ångströms X-ray crystal structure of NAD- and intermediate- bound alpha-aminomuconate-epsilon-semialdehyde dehydrogenase from pseudomonas fluorescens
Analyse 1.94 ångströms X-ray crystal structure of NAD- and intermediate- bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NPI
- Type
- protein
- Length
- 1,932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-aminomuconate 6-semialdehyde dehydrogenase
- UniProt
- Q83V33
- Ligands
- NAD, 2VS, NA
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 483 | 42% helix, 23% strand | Q83V33 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 2VS · (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.87 | 0.89 | 106 | empty |
| 2 | 835 | 0.86 | 0.89 | 106 | empty |
| 3 | 938 | 0.86 | 0.87 | 68 | empty |
| 4 | 445 | 0.76 | 0.85 | 54 | empty |
| 5 | 435 | 0.75 | 0.85 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2594 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2571 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 827 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4NPI · 1.94 Angstroms X-ray crystal structure of NAD- and intermediate- bound… · 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 Q83V33
- Elsewhere: RCSB PDB 4NPI · PDBe 4NPI · UniProt Q83V33
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