Research workbench
Crystal structure analysis of yeast hypothetical protein: YJG8_YEAST
Analyse Crystal structure analysis of yeast hypothetical protein: YJG8_YEAST in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PV1
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 33.9 kda esterase in SMC3-MRPL8 intergenic region
- EC
- 3.1.1.-
- UniProt
- P40363
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical 33.9 kda esterase in SMC3-MRPL8 intergenic region (EC 3.1.1.-) | protein | 290 | 33% helix, 20% strand | P40363 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.58 | 0.86 | 21 | empty |
| 2 | 138 | 0.46 | 0.77 | 25 | empty |
| 3 | 157 | 0.46 | 0.75 | 24 | empty |
| 4 | 137 | 0.45 | 0.76 | 24 | empty |
| 5 | 148 | 0.44 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 958 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 934 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1PV1 · Crystal Structure Analysis of Yeast Hypothetical Protein: YJG8_YEAST · the same entry in another collection · chain B against B, TM-score 1.00
- P40363 · AlphaFold monomer V2.0 prediction for S-formylglutathione hydrolase (P40363) · 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 P40363
- Elsewhere: RCSB PDB 1PV1 · PDBe 1PV1 · UniProt P40363
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