5UD6

Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound

PDB DOI: https://doi.org/10.2210/pdb5UD6/pdb

Classification: LYASE
Organism(s): Cyanidioschyzon merolae strain 10D
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-23 Released: 2017-12-27
Deposition Author(s): Watkin, S., Keown, J.R., Pearce, F.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound

Watkin, S., Keown, J.R., Pearce, F.G.

To be published.

Macromolecule Content

Total Structure Weight: 141.82 kDa
Atom Count: 9,135
Modelled Residue Count: 1,194
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	327	Cyanidioschyzon merolae strain 10D	Mutation(s): 0 Gene Names: CYME_CME179C EC: 4.3.3.7
UniProt
Find proteins for M1V4H9 (Cyanidioschyzon merolae (strain NIES-3377 / 10D)) Explore M1V4H9 Go to UniProtKB: M1V4H9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M1V4H9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]