Download MendeleyCrystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis.
Libreros, G.A., Dias, M.V.B.To be published.
7KEM
Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis
- PDB DOI: https://doi.org/10.2210/pdb7KEM/pdb
- Classification: TRANSFERASE
- Organism(s): Mycobacterium tuberculosis H37Rv
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-10-11 Released: 2020-11-18
- Funding Organization(s): Fundacao para a Ciencia e a Tecnologia
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.275
- R-Value Work: 0.261
- R-Value Observed: 0.262
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| L,D-transpeptidase 2 | 408 | Mycobacterium tuberculosis H37Rv | Mutation(s): 0 Gene Names: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 EC: 2.3.2 |  | |
UniProt | |||||
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2 Go to UniProtKB: I6Y9J2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | I6Y9J2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0JC Query on 0JC | C [auth A] D [auth A] E [auth A] F [auth A] J [auth B] | Di-mu-iodobis(ethylenediamine)diplatinum(II) C4 H16 I2 N4 Pt2 XXLKNYJQAYMQHB-UHFFFAOYSA-N |  | ||
| PT Query on PT | I [auth B] | PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N |  | ||
| 6CL Query on 6CL | H [auth B] | 6-CARBOXYLYSINE C7 H15 N2 O4 GMKMEZVLHJARHF-SYDPRGILSA-O |  | ||
| DGL Query on DGL | G [auth A] | D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.275
- R-Value Work: 0.261
- R-Value Observed: 0.262
- Space Group: I 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 117.528 | α = 90 |
| b = 121.051 | β = 90 |
| c = 122.699 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Aimless | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-11-18 Deposition Author(s): Libreros, G.A., Dias, M.V.B.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Fundacao para a Ciencia e a Tecnologia | Portugal | 2010/15971-3 |
Revision History (Full details and data files)
- Version 1.0: 2020-11-18
Type: Initial release - Version 1.1: 2023-10-18
Changes: Advisory, Author supporting evidence, Data collection, Database references, Refinement description
