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Crystal structure of thioesterase superfamily (YP_509914.1) from jannaschia sp. CCS1 at 2.00 a resolution
Analyse Crystal structure of thioesterase superfamily (YP_509914.1) from jannaschia sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NUJ
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioesterase superfamily
- UniProt
- Q28QX3
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioesterase superfamily | protein | 159 | 23% helix, 35% strand | Q28QX3 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.65 | 0.86 | 22 | empty |
| 2 | 135 | 0.64 | 0.87 | 22 | empty |
| 3 | 151 | 0.50 | 0.79 | 21 | MPD |
| 4 | 100 | 0.45 | 0.78 | 15 | MPD |
| 5 | 103 | 0.43 | 0.77 | 15 | MPD |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2NUJ · Crystal structure of thioesterase superfamily (YP_509914.1) from Jannaschia Sp. CCS1 at… · 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 Q28QX3
- Elsewhere: RCSB PDB 2NUJ · PDBe 2NUJ · UniProt Q28QX3
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