1ZVW
The Crystal Structure of TrpD (Rv2192c) from Mycobacterium tuberculosis in Complex with PRPP and Magnesium
- PDB DOI: https://doi.org/10.2210/pdb1ZVW/pdb
- Classification: TRANSFERASE
- Organism(s): Mycobacterium tuberculosis
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2005-06-02 Released: 2006-01-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.255
- R-Value Work: 0.194
- R-Value Observed: 0.197
This is version 2.0 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Anthranilate phosphoribosyltransferase | 378 | Mycobacterium tuberculosis | Mutation(s): 8 Gene Names: trpD EC: 2.4.2.18 |  | |
UniProt | |||||
Find proteins for P9WFX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX5 Go to UniProtKB: P9WFX5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P9WFX5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PRP Query on PRP | E [auth A] | 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N |  | ||
| BEN Query on BEN | F [auth A] | BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A], D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.255
- R-Value Work: 0.194
- R-Value Observed: 0.197
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.417 | α = 90 |
| b = 82.076 | β = 90 |
| c = 118.873 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2006-01-17 Deposition Author(s): Lee, C.E., Lott, J.S., Baker, E.N., Arcus, V.L., Javid-Majd, F., Goodfellow, C., Hung, L.-W., TB Structural Genomics Consortium (TBSGC)
Revision History (Full details and data files)
- Version 1.0: 2006-01-17
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 2.0: 2021-08-04
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
