Research workbench
Crystal structure of 2-hydroxymuconate-6-semialdehyde derived intermediate in NAD(+)-bound 2-aminomuconate 6-semialdehyde dehydrogenase N169D
Analyse Crystal structure of 2-hydroxymuconate-6-semialdehyde derived intermediate in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KLM
- 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, NA
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 484 | 42% helix, 23% strand | Q83V33 |
| B, C | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 483 | 42% helix, 23% strand | Q83V33 |
| D | 2-aminomuconate 6-semialdehyde dehydrogenase | protein | 482 | 42% helix, 24% strand | Q83V33 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.86 | 0.88 | 71 | empty |
| 2 | 1028 | 0.85 | 0.86 | 116 | empty |
| 3 | 398 | 0.85 | 0.93 | 55 | empty |
| 4 | 429 | 0.76 | 0.85 | 52 | empty |
| 5 | 425 | 0.76 | 0.85 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2597 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2587 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 825 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 820 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 804 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KLM · Crystal structure of 2-hydroxymuconate-6-semialdehyde derived intermediate in… · 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 5KLM · PDBe 5KLM · UniProt Q83V33
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