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Here's a summary of the PDB file:
AF-A0A6F8Z204-F1-model_v6.pdb
File type: AlphaFold2 predicted protein structure (PDB format)
Protein Identity
| Field | Value |
|---|---|
| Protein name | NADP-dependent oxidoreductase |
| UniProt ID | A0A6F8Z204 |
| Organism | Streptomyces violaceusniger (TaxID: 68280) |
| Chain | A |
| Sequence length | 339 residues (positions 1-339) |
| Prediction date | June 1, 2022 |
| Model version | AlphaFold Monomer v2.0 |
Structure
- Single polypeptide chain (Chain A)
- Contains ATOM records for all heavy atoms with 3D coordinates (X, Y, Z)
- The B-factor column encodes pLDDT confidence scores (per-residue confidence, 0-100):
- Residues seen in the sample range from ~88 to ~97 pLDDT, indicating high to very high confidence
- Standard PDB format with backbone and sidechain atoms for each residue
Biological Context
NADP-dependent oxidoreductases are enzymes that catalyze redox reactions using NADP+/NADPH as a cofactor. In Streptomyces violaceusniger (a soil-dwelling actinobacterium known for producing bioactive compounds), this enzyme likely plays a role in biosynthetic or metabolic redox pathways.
Citation
The structure was predicted by AlphaFold2 (Jumper et al., Nature 596, 583, 2021; PMID: 34265844), under a CC-BY 4.0 licence.
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Generated Files
Static Images (rendered now, no software needed)
- - 3D backbone trace colored by pLDDT
AF A0A6F8Z204 structure
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- - Per-residue confidence bar chart
AF A0A6F8Z204 plddt
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Visualization Scripts
| File | Tool | Usage |
|---|---|---|
visualize pymol PML File · PML | PyMOL | pymol visualize_pymol.pml |
visualize chimerax CXC File · CXC | UCSF ChimeraX | chimerax --script visualize_chimerax.cxc |
visualize matplotlib Python File · PY | Python/matplotlib | python3 visualize_matplotlib.py |
Key Stats from the PDB
| Metric | Value |
|---|---|
| Cα atoms parsed | 339 |
| Mean pLDDT | 96.3 (very high confidence overall) |
| Min pLDDT | 50.1 |
| Max pLDDT | 98.9 |
A mean pLDDT of 96.3 is excellent - almost the entire structure is predicted with very high confidence (>90), which is typical for compact enzyme domains. The few lower-confidence residues (near 50) are likely flexible loops.
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