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Crystal structure of a putative thioesterase (TM1040_2492) from silicibacter sp. TM1040 at 1.79 a resolution
Analyse Crystal structure of a putative thioesterase (TM1040_2492) from silicibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PBL
- Type
- protein
- Length
- 1,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ESTERASE/LIPASE/THIOESTERASE
- UniProt
- Q1GDP2
- Ligands
- UNL, MG, CL, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative ESTERASE/LIPASE/THIOESTERASE | protein | 262 | 42% helix, 18% strand | Q1GDP2 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains B, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.78 | 0.80 | 131 | MG |
| 2 | 800 | 0.74 | 0.79 | 68 | CL |
| 3 | 819 | 0.74 | 0.79 | 71 | CL |
| 4 | 104 | 0.46 | 0.79 | 22 | UNL |
| 5 | 118 | 0.44 | 0.77 | 20 | UNL |
Interfaces
4 interfaces between chains.
- C–D · 559 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2PBL · Crystal structure of a putative thioesterase (tm1040_2492) 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 Q1GDP2
- Elsewhere: RCSB PDB 2PBL · PDBe 2PBL · UniProt Q1GDP2
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