Research workbench
Crystal structure of C173S mutation in the PMGL2 esterase from permafrost metagenomic library
Analyse Crystal structure of C173S mutation in the PMGL2 esterase from permafrost… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZL7
- Type
- protein
- Length
- 636 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
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PMGL2 (EC 3.1.1.3) | protein | 317 | 41% helix, 15% strand | A0A142J6I6 |
| B | PMGL2 (EC 3.1.1.3) | protein | 319 | 42% helix, 15% strand | A0A142J6I6 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.78 | 0.82 | 85 | PG6 |
| 2 | 680 | 0.72 | 0.78 | 61 | PG6 |
| 3 | 135 | 0.42 | 0.76 | 32 | MG |
| 4 | 79 | 0.37 | 0.76 | 17 | empty |
| 5 | 73 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1573 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6ZL7 · Crystal structure of C173S mutation in the PMGL2 esterase from permafrost metagenomic… · 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 6ZL7 · PDBe 6ZL7 · UniProt A0A142J6I6
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