Download MendeleyE.Coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE
Arendall, W.B., Hyatt, D.C., Roberts, S.A., Dahlgran, A.L., Maley, F., Montfort, W.R.To be published.
3BFI
E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP
- PDB DOI: https://doi.org/10.2210/pdb3BFI/pdb
- Classification: TRANSFERASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-11-21 Released: 2008-12-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.218
- R-Value Work: 0.165
- R-Value Observed: 0.168
Starting Model: experimental
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This is version 1.6 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 |
| Thymidylate synthase | 264 | Escherichia coli | Mutation(s): 1 Gene Names: thyA EC: 2.1.1.45 |  | |
UniProt | |||||
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884 Go to UniProtKB: P0A884 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0A884 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NDU Query on NDU | C [auth A] | 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O10 P ZYBJIJYGXJSDTC-XZBKPIIZSA-N |  | ||
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CXM Query on CXM | A | L-PEPTIDE LINKING | C6 H11 N O4 S |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 ?
- R-Value Free: 0.218
- R-Value Work: 0.165
- R-Value Observed: 0.168
- Space Group: I 21 3
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 133.02 | ¦Á = 90 |
| b = 133.02 | ¦Â = 90 |
| c = 133.02 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MADNESS | data collection |
| PROCOR | data reduction |
| PROCOR | data scaling |
Entry History
Deposition Data
- Released Date: 2008-12-02 Deposition Author(s): Roberts, S.A., Montfort, W.R.
Revision History (Full details and data files)
- Version 1.0: 2008-12-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2018-04-18
Changes: Data collection - Version 1.4: 2021-10-20
Changes: Database references, Derived calculations - Version 1.5: 2023-08-30
Changes: Data collection, Refinement description - Version 1.6: 2024-11-20
Changes: Structure summary
