MolNFT v1 · #143439 · protein
A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (spin)
6AZP · Myeloperoxidase: “A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (spin)”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 5 pockets (best druggability 0.79). MolNFT v1 #143439 on…
- PDB
- 6AZP
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase; Staphylococcal peroxidase inhibitor
- EC
- 1.11.2.2
- UniProt
- P05164, A0A1K8H768
- Ligands
- NAG, BMA, CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 577 | 40% helix, 9% strand | P05164 |
| B | Staphylococcal peroxidase inhibitor | protein | 57 | 53% helix, 0% strand | A0A1K8H768 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.79 | 0.80 | 83 | empty |
| 2 | 69 | 0.40 | 0.80 | 20 | empty |
| 3 | 100 | 0.36 | 0.75 | 23 | empty |
| 4 | 55 | 0.29 | 0.75 | 15 | empty |
| 5 | 51 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, glycosylation, oxidation).
Compared structures
- 6AZP · A Structurally Dynamic N-terminal Region Drives Function of the Staphylococcal Peroxidase… · the same entry in another collection · chain A against A, TM-score 1.00
- P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain A against A, TM-score 0.98
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
- Every structure of UniProt A0A1K8H768
- Elsewhere: RCSB PDB 6AZP · PDBe 6AZP · UniProt P05164 · UniProt A0A1K8H768
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