Download MendeleyDrugscore FP: Profiling Protein-Ligand Interactions using Fingerprint Simplicity paired with Knowledge-Based Potential Fields
Pfeffer, P., Neudert, G., Englert, L., Ritschel, T., Baum, B., Klebe, G.To be published.
3FGD | pdb_00003fgd
Drugscore FP: Thermoylsin in complex with fragment.
- PDB DOI: https://doi.org/10.2210/pdb3FGD/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus thermoproteolyticus
- Mutation(s): No
- Deposited: 2008-12-05 Released: 2009-12-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.189 (Depositor), 0.140 (DCC)
- R-Value Work: 0.146 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.148 (Depositor)
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thermolysin | 316 | Bacillus thermoproteolyticus | Mutation(s): 0 EC: 3.4.24.27 |  | |
UniProt | |||||
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800 Go to UniProtKB: P00800 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00800 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BYA Query on BYA | G [auth A] | N-(phenylcarbonyl)-beta-alanine C10 H11 N O3 CWXYHOHYCJXYFQ-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | H [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CA Query on CA | B [auth A], C [auth A], D [auth A], E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.189 (Depositor), 0.140 (DCC)
- R-Value Work: 0.146 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.148 (Depositor)
Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 92.6 | α = 90 |
| b = 92.6 | β = 90 |
| c = 128.673 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SHELXL-97 | refinement |
| CNS | refinement |
| MAR345dtb | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2009-12-15 Deposition Author(s): Englert, L., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2009-12-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2019-07-24
Changes: Data collection, Refinement description - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
