MolNFT v1 · #171034 · protein
Dye-type peroxidase dtpb in the ferryl state: spectroscopically validated composite structure
6YR4 · Putative iron-dependent peroxidase: “Dye-type peroxidase dtpb in the ferryl state: spectroscopically validated composite structure”. X-ray diffraction, 3 ligands (HEM, MG, O), 16 pockets (best druggability 0.83). MolNFT v1 #171034…
- PDB
- 6YR4
- Type
- protein
- Length
- 1,832 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative iron-dependent peroxidase
- UniProt
- A0A1H2DDB9
- Ligands
- HEM, MG, O
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 26% strand | A0A1H2DDB9 |
| B | Putative iron-dependent peroxidase | protein | 305 | 31% helix, 27% strand | A0A1H2DDB9 |
| D | Putative iron-dependent peroxidase | protein | 303 | 31% helix, 26% strand | A0A1H2DDB9 |
| F | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 26% strand | A0A1H2DDB9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, C
- O · Oxygen atom · ion · 6 copies · chains A, B, C, D, E, F
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.83 | 0.86 | 86 | HEM, O |
| 2 | 890 | 0.83 | 0.85 | 93 | empty |
| 3 | 888 | 0.82 | 0.84 | 81 | empty |
| 4 | 843 | 0.81 | 0.84 | 91 | HEM, O |
| 5 | 1071 | 0.80 | 0.82 | 110 | HEM, O |
Interfaces
12 interfaces between chains.
- B–E · 1177 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1112 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1105 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 566 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6YR4 · Dye-type peroxidase DtpB in the ferryl state: Spectroscopically Validated composite… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1H2DDB9
- Elsewhere: RCSB PDB 6YR4 · PDBe 6YR4 · UniProt A0A1H2DDB9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.