MolNFT v1 · #87446 · protein
Myeloperoxidase in complex with the revesible inhibitor HX1
4C1M · Myeloperoxidase light chain: “Myeloperoxidase in complex with the revesible inhibitor HX1”. X-ray diffraction, 9 ligands (HEM, NIH, NAG), 10 pockets (best druggability 0.80). MolNFT v1 #87446 on GenesisL1: 3D structure, binding…
- PDB
- 4C1M
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase light chain; Myeloperoxidase heavy chain
- EC
- 1.11.2.2, 1.11.1.7
- UniProt
- P05164
- Ligands
- HEM, NIH, NAG, MAN, BMA, FUC, CA, SO4, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase light chain (EC 1.11.2.2, 1.11.1.7) | protein | 101 | 26% helix, 11% strand | P05164 |
| B | Myeloperoxidase light chain (EC 1.11.2.2, 1.11.1.7) | protein | 104 | 25% helix, 11% strand | P05164 |
| C, D | Myeloperoxidase heavy chain (EC 1.11.2.2, 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
- NIH · 2-{[3,5-bis(trifluoromethyl)benzyl]amino}-N-hydroxy-6-oxo-1,6-dihydropyrimidine-5-carboxamide · 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
- SO4 · Sulfate ion · ion · 2 copies · chains B, D, C
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 5 copies · chains C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.80 | 0.84 | 67 | FUC, MAN |
| 2 | 843 | 0.80 | 0.82 | 67 | HEM, NIH |
| 3 | 859 | 0.80 | 0.82 | 66 | HEM, NIH |
| 4 | 106 | 0.49 | 0.81 | 26 | empty |
| 5 | 75 | 0.46 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5704 Ų buried · 107 hydrogen bonds · protein-protein
- B–D · 5654 Ų buried · 108 hydrogen bonds · protein-protein
- A–B · 618 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 384 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan, 5 cofactor, 2 modified (disulfide, N-glycosylation, heme attachment, 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 4C1M · PDBe 4C1M · UniProt P05164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.