Research workbench
Crystal structure of the PMGL2 esterase from permafrost metagenomic library
Analyse Crystal structure of the PMGL2 esterase from permafrost metagenomic library in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QIN
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PMGL2
- EC
- 3.1.1.3
- UniProt
- A0A142J6I6
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PMGL2 (EC 3.1.1.3) | protein | 312 | 41% helix, 15% strand | A0A142J6I6 |
| B | PMGL2 (EC 3.1.1.3) | protein | 318 | 41% helix, 15% strand | A0A142J6I6 |
Ligands and binding sites
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 | 139 | 0.77 | 0.95 | 29 | empty |
| 2 | 674 | 0.72 | 0.79 | 61 | empty |
| 3 | 623 | 0.72 | 0.79 | 60 | empty |
| 4 | 132 | 0.43 | 0.76 | 32 | CL, MG |
| 5 | 69 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1489 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6QIN · Crystal structure of the PMGL2 esterase from permafrost metagenomic library · 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 A0A142J6I6
- Elsewhere: RCSB PDB 6QIN · PDBe 6QIN · UniProt A0A142J6I6
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