7V8T | pdb_00007v8t

Crystal structure of class II pyruvate aldolase from Pseudomonas aeruginosa.

PDB DOI: https://doi.org/10.2210/pdb7V8T/pdb

Classification: LYASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-23 Released: 2022-08-24
Deposition Author(s): Seo, P.W., Kim, J.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.227 (Depositor), 0.225 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical and Molecular Characterization of Pyruvate Aldolase for the Synthesis of 2-Keto-4-hydroxybutyrate.

Jeong, Y.J., Le, T.K., Seo, P.W., Ju, S.B., Kim, J.S., Yeom, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 171.21 kDa
Atom Count: 11,711
Modeled Residue Count: 1,518
Deposited Residue Count: 1,608
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase	A, B, C, D, E A, B, C, D, E, F	268	Pseudomonas aeruginosa	Mutation(s): 0 EC: 4.1.2.52 (PDB Primary Data), 4.1.2 (UniProt)
UniProt
Find proteins for A0A081HJP9 (Pseudomonas aeruginosa) Explore A0A081HJP9 Go to UniProtKB: A0A081HJP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A081HJP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G (Subject of Investigation/LOI) Query on P6G Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth F] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth F] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth F]	H [auth A], Q [auth F]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain Q [auth F]
IOD (Subject of Investigation/LOI) Query on IOD Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A] I [auth A] J [auth B] K [auth B] L [auth C] G [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth E], P [auth E], R [auth F]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F]