Research workbench
X-ray structure of yjhp from E.COLI northeast structural genomics research consortium (nesg) target ER13
Analyse X-ray structure of yjhp from E.COLI northeast structural genomics research… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NKV
- Type
- protein
- Length
- 725 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yjhp
- UniProt
- P39367
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein yjhp | protein | 245 | 43% helix, 21% strand | P39367 |
| B | Hypothetical protein yjhp | protein | 231 | 42% helix, 19% strand | P39367 |
| C | Hypothetical protein yjhp | protein | 249 | 40% helix, 19% strand | P39367 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.81 | 0.83 | 104 | empty |
| 2 | 607 | 0.73 | 0.80 | 58 | empty |
| 3 | 319 | 0.59 | 0.77 | 47 | empty |
| 4 | 290 | 0.59 | 0.78 | 40 | empty |
| 5 | 199 | 0.57 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 917 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 899 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 861 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 1NKV · X-ray structure of yjhp from E.COLI northeast structural genomics research consortium… · the same entry in another collection · chain A against A, TM-score 1.00
- P39367 · AlphaFold monomer V2.0 prediction for uncharacterized protein yjhp (P39367) · 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 P39367
- Elsewhere: RCSB PDB 1NKV · PDBe 1NKV · UniProt P39367
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