MolNFT v1 · #171043 · protein
Sfx structure of dye-type peroxidase dtpb in the ferryl state
6YRD · Putative iron-dependent peroxidase: “Sfx structure of dye-type peroxidase dtpb in the ferryl state”. X-ray diffraction, 3 ligands (HEM, MG, O), 20 pockets (best druggability 0.85). MolNFT v1 #171043 on GenesisL1: 3D structure…
- PDB
- 6YRD
- Type
- protein
- Length
- 1,830 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
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Putative iron-dependent peroxidase | protein | 305 | 31% helix, 26% strand | A0A1H2DDB9 |
| B | Putative iron-dependent peroxidase | protein | 304 | 32% helix, 27% strand | A0A1H2DDB9 |
| C | 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
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.85 | 0.86 | 111 | empty |
| 2 | 925 | 0.85 | 0.86 | 111 | empty |
| 3 | 820 | 0.82 | 0.85 | 87 | HEM, O |
| 4 | 826 | 0.82 | 0.84 | 95 | HEM, O |
| 5 | 887 | 0.80 | 0.83 | 82 | HEM, O |
Interfaces
12 interfaces between chains.
- B–E · 1306 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1209 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 591 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 584 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YRD · SFX structure of dye-type peroxidase DtpB in the ferryl state · 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 6YRD · PDBe 6YRD · UniProt A0A1H2DDB9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.