6R62 | pdb_00006r62

Crystal structure of a class II pyruvate aldolase from Sphingomonas wittichii RW1 in complex with hydroxypyruvate

PDB DOI: https://doi.org/10.2210/pdb6R62/pdb

Classification: LYASE
Organism(s): Rhizorhabdus wittichii RW1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-26 Released: 2019-05-29
Deposition Author(s): Marsden, S.R., Mestrom, L., Hagedoorn, P.L., Bento, I., McMillan, D.G.G., Hanefeld, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.185 (Depositor), 0.190 (DCC)
R-Value Work:
0.164 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

CH-Pi Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase

Marsden, S.R., Mestrom, L., Bento, I., Hagedoorn, P.L., McMillan, D.G.G., Hanefeld, U.

(2019) Adv Synth Catal

DOI: https://doi.org/10.1002/adsc.201900205

Macromolecule Content

Total Structure Weight: 27.34 kDa
Atom Count: 2,305
Modeled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HpcH/HpaI aldolase	A	252	Rhizorhabdus wittichii RW1	Mutation(s): 0 Gene Names: Swit_5035 EC: 4.1.2
UniProt
Find proteins for A0A9J9HGY6 (Rhizorhabdus wittichii (strain DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1)) Explore A0A9J9HGY6 Go to UniProtKB: A0A9J9HGY6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9J9HGY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PY Query on 3PY Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	3-HYDROXYPYRUVIC ACID C₃ H₄ O₄ HHDDCCUIIUWNGJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]