5D09 | pdb_00005d09

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant

PDB DOI: https://doi.org/10.2210/pdb5D09/pdb

Classification: TRANSFERASE
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-08-02 Released: 2016-08-10
Deposition Author(s): Heyes, L.C., Parker, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.210 (Depositor), 0.220 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant at 2.35 Angstroms resolution

Heyes, L.C., Parker, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 155.34 kDa
Atom Count: 10,453
Modeled Residue Count: 1,330
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospho-2-dehydro-3-deoxyheptonate aldolase	A, B, C, D	351	Neisseria meningitidis MC58	Mutation(s): 1 Gene Names: aroG, NMB0307 EC: 2.5.1.54
UniProt
Find proteins for Q9K169 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K169 Go to UniProtKB: Q9K169
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEP Query on PEP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	I [auth B], L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain I [auth B] Focus chain L [auth C]
TMO Query on TMO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	trimethylamine oxide C₃ H₉ N O UYPYRKYUKCHHIB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	J [auth B], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain J [auth B] Focus chain M [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]