MolNFT v1 · #110719 · protein
Crystal structure of buffalo lactoperoxidase with rhodanide at 2.09 ångström resolution
4Y55: “Crystal structure of buffalo lactoperoxidase with rhodanide at 2.09 ångström resolution”. X-ray diffraction, 8 ligands (HEM, NAG, BMA), 7 pockets (best druggability 0.80). MolNFT v1 #110719 on GenesisL1: 3D structure, binding sites…
- PDB
- 4Y55
- 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
- Ligands
- HEM, NAG, BMA, MAN, CA, IOD, NO3, SCN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 8% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 6 copies · chains A
- NO3 · Nitrate ion · ion · 4 copies · chains A
- SCN · Thiocyanate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.80 | 0.81 | 130 | IOD, HEM, SCN |
| 2 | 105 | 0.45 | 0.79 | 20 | empty |
| 3 | 76 | 0.37 | 0.77 | 14 | IOD |
| 4 | 84 | 0.36 | 0.76 | 18 | empty |
| 5 | 50 | 0.35 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 4Y55 · Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution · 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
- Elsewhere: RCSB PDB 4Y55 · PDBe 4Y55
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