7JZA

Dihydrodipicolinate synthase S48F mutant with lysine in the allosteric site, and pyruvate and succinic semi-aldehyde in the catalytic site

PDB DOI: https://doi.org/10.2210/pdb7JZA/pdb

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-09-01 Released: 2021-09-22
Deposition Author(s): Board, A.J., Dobson, R.C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.165
R-Value Work: 0.136
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mapping the uncharted water channel of DHDPS

Board, A.J., Dobson, R.C.J.

To be published.

Macromolecule Content

Total Structure Weight: 63.76 kDa
Atom Count: 5,165
Modelled Residue Count: 584
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	292	Escherichia coli	Mutation(s): 1 Gene Names: dapA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920... dapA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920, BANRA_01022, BANRA_04600, BMA87_04055, BUE81_00170, BvCms2454_00575, BvCmsKSP026_00126, BvCmsSINP011_00590, BW690_08395, BZL31_19835, C5N07_10510, C9306_12515, C9Z39_22035, C9Z89_01665, CG692_24655, CI693_08805, CIG45_08195, COD30_00655, D2185_06295, D3821_11825, D4638_04510, D4718_03620, D5H35_00590, D6004_00600, D9610_05430, D9D44_02140, D9I18_08280, D9J52_02245, D9S45_15015, DAH30_02905, DAH32_09095, DIV22_31750, DJ503_11770, DL326_03925, DL530_01595, DL800_18800, DLW60_01905, DMY83_09445, DNW42_05980, DQF71_00895, DS143_00895, DT034_06790, DTL43_01515, DVB38_05855, E2119_05140, E2134_09475, E2135_00560, E2855_03226, E2863_03133, E5P22_02280, E5S42_08940, EAI42_12285, EAI52_02575, EAM59_02025, EAN70_00660, EBM08_03910, EC3234A_44c00840, EC95NR1_01697, ECTO6_01408, ED307_17520, ED600_00625, EEP23_23010, EG599_00615, EH412_01980, EHJ36_02055, EI028_07440, EIZ93_19645, EKI52_22350, EL75_1173, EL79_1184, EL80_1189, EPT01_15155, ERS150876_00779, EYD11_06580, F1E19_01790, F7F00_00605, F7F23_09350, F7F26_01975, FQR64_06700, GHR40_11105, GKF74_08320, GKF86_10525, GKF89_17025, GP666_02180, GP935_11985, GQA06_13610, GQE30_13075, GQE34_24640, GQE51_05930, GRW80_06100, NCTC10963_01382, NCTC11126_06127, NCTC11341_00817, NCTC13216_00544, NCTC8960_04113, NCTC9045_01668, NCTC9062_01738, NCTC9962_06536, RK56_024520, SAMEA3472047_03904, SAMEA3484427_00338, SAMEA3484429_00447, SAMEA3752559_00798, SAMEA3753300_00971, SK85_02727 EC: 4.3.3.7
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2 Go to UniProtKB: P0A6L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth B]	C [auth A], G [auth B], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain J [auth B]