Research workbench
Structure of shikimate 5-dehydrogenase-like protein HI0607
Analyse Structure of shikimate 5-dehydrogenase-like protein HI0607 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NPY
- Type
- protein
- Length
- 1,079 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical shikimate 5-dehydrogenase-like protein HI0607
- UniProt
- P44774
- Ligands
- ACE
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical shikimate 5-dehydrogenase-like protein HI0607 | protein | 269 | 40% helix, 19% strand | P44774 |
| B, C, D | Hypothetical shikimate 5-dehydrogenase-like protein HI0607 | protein | 270 | 39% helix, 19% strand | P44774 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.66 | 0.77 | 54 | ACE |
| 2 | 515 | 0.66 | 0.77 | 54 | empty |
| 3 | 475 | 0.65 | 0.77 | 41 | empty |
| 4 | 486 | 0.64 | 0.77 | 48 | empty |
| 5 | 79 | 0.36 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 307 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1NPY · Structure of shikimate 5-dehydrogenase-like protein HI0607 · the same entry in another collection · chain A against A, TM-score 1.00
- P44774 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase-like protein HI_0607… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P44774
- Elsewhere: RCSB PDB 1NPY · PDBe 1NPY · UniProt P44774
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