Research workbench
Crystal structure of bromide-bound human myeloperoxidase isoform C at pH 5.5
Analyse Crystal structure of bromide-bound human myeloperoxidase isoform C at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D2V
- 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, BR, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 43% helix, 8% 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
- BR · Bromide ion · ion · 8 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
- ACT · Acetate ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.81 | 0.84 | 55 | BR, HEM |
| 2 | 704 | 0.80 | 0.84 | 67 | MAN |
| 3 | 864 | 0.80 | 0.82 | 67 | BR, HEM |
| 4 | 91 | 0.48 | 0.82 | 26 | empty |
| 5 | 75 | 0.47 | 0.83 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5719 Ų buried · 113 hydrogen bonds · protein-protein
- B–D · 5669 Ų buried · 112 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 2 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
- 1D2V · Crystal structure of bromide-bound human myeloperoxidase isoform C at pH 5.5 · 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 C 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
- Elsewhere: RCSB PDB 1D2V · PDBe 1D2V · UniProt P05164
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