Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Probable 2-keto-3-deoxy-galactonate aldolase YagE | A, B, C, D | 343 | Escherichia coli K-12 | Mutation(s): 0  Gene Names: b0268, JW0261, yagE EC: 4.1.2 (PDB Primary Data), 4.1.2.51 (UniProt), 4.1.2.28 (UniProt) | ![]() |
UniProt | |||||
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682  Go to UniProtKB:  P75682 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P75682 | ||||
Protein Feature ViewExpand | |||||
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Ligands 7 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GXS Query on GXS | UA [auth D], Y [auth B] | (4R)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-GSVOUGTGSA-N | Ligand Interaction | ||
GXP Query on GXP | TA [auth D], X [auth B] | (4S)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-VKHMYHEASA-N | Ligand Interaction | ||
GOL Query on GOL | AA [auth C], F [auth A], P [auth B], Q [auth B], QA [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | Ligand Interaction | ||
PYR Query on PYR | KA [auth C], N [auth A] | PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N | Ligand Interaction | ||
EDO Query on EDO | CA [auth C], DA [auth C], E [auth A], EA [auth C], FA [auth C], | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | Ligand Interaction | ||
GXT Query on GXT | M [auth A] | ethanedial C2 H2 O2 LEQAOMBKQFMDFZ-UHFFFAOYSA-N | Ligand Interaction | ||
MG Query on MG | BA [auth C], H [auth A], RA [auth D], S [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | Ligand Interaction |
Length ( Å ) | Angle ( ˚ ) |
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a = 141.24 | α = 90 |
b = 155.14 | β = 90 |
c = 55.58 | γ = 90 |
Software Name | Purpose |
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PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |