Research workbench
Crystal structure of the complex of goat lactoperoxidase with 3- hydroxymethyl phenol at 1.98 ångström resolution
Analyse Crystal structure of the complex of goat lactoperoxidase with 3- hydroxymethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MSF
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- A3F9D6
- Ligands
- HEM, 3HY, NAG, CA, IOD, SCN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 10% strand | A3F9D6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 3HY · 3-(hydroxymethyl)phenol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 15 copies · chains A
- SCN · Thiocyanate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 993 | 0.80 | 0.81 | 82 | HEM, IOD, SCN, 3HY |
| 2 | 335 | 0.60 | 0.77 | 57 | EDO |
| 3 | 118 | 0.48 | 0.79 | 24 | empty |
| 4 | 85 | 0.39 | 0.78 | 29 | empty |
| 5 | 71 | 0.36 | 0.77 | 15 | IOD |
Modifications
Observed in the structure: 7 disulfide, 2 glycan, 1 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 4MSF · Crystal structure of the complex of goat lactoperoxidase with 3-hydroxymethyl phenol at… · 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 A3F9D6
- Elsewhere: RCSB PDB 4MSF · PDBe 4MSF · UniProt A3F9D6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.