Research workbench
Crystal structure of a putative thioesterase (TM1040_1390) from silicibacter sp. TM1040 at 2.15 a resolution
Analyse Crystal structure of a putative thioesterase (TM1040_1390) from silicibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QWZ
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetic acid degradation-related protein
- UniProt
- Q1GGU3
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylacetic acid degradation-related protein | protein | 144 | 26% helix, 34% strand | Q1GGU3 |
| C | Phenylacetic acid degradation-related protein | protein | 138 | 28% helix, 36% strand | Q1GGU3 |
| D | Phenylacetic acid degradation-related protein | protein | 137 | 23% helix, 36% strand | Q1GGU3 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.72 | 0.76 | 94 | GOL, ACT |
| 2 | 877 | 0.70 | 0.75 | 76 | ACT, GOL |
| 3 | 68 | 0.34 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–D · 754 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 753 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 179 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 2QWZ · Crystal structure of a putative thioesterase (TM1040_1390) from silicibacter sp. TM1040… · 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 Q1GGU3
- Elsewhere: RCSB PDB 2QWZ · PDBe 2QWZ · UniProt Q1GGU3
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