MolNFT v1 · #171042 · protein
Spectroscopically-validated structure of dtpb from streptomyces lividans in the ferric state
6YRC · Putative iron-dependent peroxidase: “Spectroscopically-validated structure of dtpb from streptomyces lividans in the ferric state”. X-ray diffraction, 2 ligands (HEM, MG), 20 pockets (best druggability 0.84). MolNFT v1 #171042 on…
- PDB
- 6YRC
- Type
- protein
- Length
- 1,838 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
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 26% strand | A0A1H2DDB9 |
| D | Putative iron-dependent peroxidase | protein | 306 | 31% helix, 25% strand | A0A1H2DDB9 |
| F | Putative iron-dependent peroxidase | protein | 308 | 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 · 5 copies · chains A, C, E, F
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 10 copies · chains A, F, B, E, D
- GOL · Glycerol · additive · 9 copies · chains B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.84 | 0.88 | 82 | GOL |
| 2 | 941 | 0.83 | 0.84 | 98 | MG, HEM, 7PE |
| 3 | 816 | 0.82 | 0.85 | 87 | HEM, GOL |
| 4 | 851 | 0.82 | 0.84 | 88 | HEM |
| 5 | 320 | 0.80 | 0.91 | 38 | HEM |
Interfaces
12 interfaces between chains.
- B–E · 1228 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1201 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1108 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 576 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6YRC · Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric… · 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 6YRC · PDBe 6YRC · UniProt A0A1H2DDB9
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