MolNFT v1 · #55997 · protein
Crystal structure of APE0912 from aeropyrum pernix K1
2Z1N · Dehydrogenase: “Crystal structure of APE0912 from aeropyrum pernix K1”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.67). MolNFT v1 #55997 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z1N
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrogenase
- UniProt
- Q9YDK1
- Ligands
- NA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrogenase | protein | 237 | 49% helix, 17% strand | Q9YDK1 |
| B | Dehydrogenase | protein | 243 | 47% helix, 17% strand | Q9YDK1 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.67 | 0.80 | 40 | empty |
| 2 | 139 | 0.47 | 0.77 | 22 | empty |
| 3 | 171 | 0.46 | 0.76 | 28 | NA |
Interfaces
1 interface between chains.
- A–B · 1619 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2Z1N · Crystal structure of APE0912 from Aeropyrum pernix K1 · 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 Q9YDK1
- Elsewhere: RCSB PDB 2Z1N · PDBe 2Z1N · UniProt Q9YDK1
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