Research workbench
Structural analyses of human myeloperoxidase-thiocyanate complex
Analyse Structural analyses of human myeloperoxidase-thiocyanate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DNU
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.1.7
- UniProt
- P05164
- Ligands
- HEM, NAG, MAN, BMA, FUC, CA, SCN, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myeloperoxidase (EC 1.11.1.7) | protein | 104 | 25% helix, 11% strand | P05164 |
| C, D | Myeloperoxidase (EC 1.11.1.7) | protein | 466 | 41% helix, 9% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, B, C, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
- SCN · Thiocyanate ion · ion · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
- ACY · Acetic acid · additive · 6 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.80 | 0.84 | 56 | SCN, HEM |
| 2 | 726 | 0.80 | 0.84 | 67 | empty |
| 3 | 733 | 0.79 | 0.83 | 55 | SCN, HEM |
| 4 | 78 | 0.53 | 0.85 | 21 | empty |
| 5 | 81 | 0.46 | 0.81 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5729 Ų buried · 104 hydrogen bonds · protein-protein
- B–D · 5648 Ų buried · 105 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 258 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 cofactor, 6 glycan, 2 modified (disulfide, heme attachment, N-glycosylation, oxidation).
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 P05164
- Elsewhere: RCSB PDB 1DNU · PDBe 1DNU · UniProt P05164
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