Research workbench
Crystallographic refinement of lignin peroxidase at 2 ångströms
Analyse Crystallographic refinement of lignin peroxidase at 2 ångströms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LGA
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lignin peroxidase
- EC
- 1.11.1.-
- UniProt
- P49012
- Ligands
- HEM, NAG, CA
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lignin peroxidase (EC 1.11.1.-) | protein | 343 | 41% helix, 6% strand | P49012 |
| B | Lignin peroxidase (EC 1.11.1.-) | protein | 341 | 42% helix, 6% strand | P49012 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.84 | 0.91 | 50 | HEM |
| 2 | 453 | 0.83 | 0.90 | 51 | HEM |
| 3 | 56 | 0.29 | 0.75 | 16 | empty |
| 4 | 62 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P49012
- Elsewhere: RCSB PDB 1LGA · PDBe 1LGA · UniProt P49012
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