MolNFT v1 · #144212 · protein
Crystal structure of a recombinant form of human myeloperoxidase bound to an inhibitor from staphylococcus delphini
6BMT: “Crystal structure of a recombinant form of human myeloperoxidase bound to an inhibitor from staphylococcus…”. X-ray diffraction, 4 ligands (HEM, NAG, CA), 9 pockets (best druggability 0.85). MolNFT v1 #144212 on GenesisL1: 3D…
- PDB
- 6BMT
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase; Hypothetical protein
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, NAG, CA, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myeloperoxidase (EC 1.11.2.2) | protein | 573 | 38% helix, 9% strand | P05164 |
| B | Hypothetical protein | protein | 70 | 44% helix, 13% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.85 | 0.95 | 44 | HEM |
| 2 | 109 | 0.56 | 0.84 | 21 | empty |
| 3 | 152 | 0.49 | 0.78 | 28 | empty |
| 4 | 74 | 0.46 | 0.82 | 21 | empty |
| 5 | 109 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 6BMT · Crystal Structure of a Recombinant form of Human Myeloperoxidase Bound to an Inhibitor… · 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 0.99
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 6BMT · PDBe 6BMT · UniProt P05164
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