MolNFT v1 · #140986 · protein
Crystal structure of aminocaproic acid cyclase in complex with NAD (+)
5YSS · 3-hydroxybutyrate dehydrogenase: “Crystal structure of aminocaproic acid cyclase in complex with NAD (+)”. X-ray diffraction, 1 ligand (NAD), 10 pockets (best druggability 0.87). MolNFT v1 #140986 on GenesisL1: 3D structure, binding…
- PDB
- 5YSS
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxybutyrate dehydrogenase
- UniProt
- A0A0D7LY80
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxybutyrate dehydrogenase | protein | 255 | 49% helix, 15% strand | A0A0D7LY80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.87 | 0.89 | 56 | empty |
| 2 | 694 | 0.73 | 0.79 | 81 | NAD |
| 3 | 419 | 0.70 | 0.81 | 39 | NAD |
| 4 | 428 | 0.66 | 0.78 | 41 | empty |
| 5 | 440 | 0.64 | 0.77 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1570 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1559 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1254 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 232 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YSS · Crystal structure of aminocaproic acid cyclase 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 A0A0D7LY80
- Elsewhere: RCSB PDB 5YSS · PDBe 5YSS · UniProt A0A0D7LY80
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