5DCB

Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP

PDB DOI: https://doi.org/10.2210/pdb5DCB/pdb

Classification: TRANSFERASE
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-23 Released: 2016-08-24
Deposition Author(s): Heyes, L.C., Parker, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.212
R-Value Work: 0.169
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with PEP at 2.05 Angstroms

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

To be published.

Macromolecule Content

Total Structure Weight: 157.21 kDa
Atom Count: 11,505
Modelled Residue Count: 1,385
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): 0 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEP Query on PEP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	K [auth A], P [auth B], T [auth C], Y [auth D]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D]
PHE Query on PHE Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	L [auth A], Q [auth B], U [auth C], Z [auth D]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Z [auth D]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain X [auth D]	I [auth A], X [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain X [auth D]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth D]	G [auth A], H [auth A], O [auth B], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain W [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	E [auth A], N [auth B], S [auth C], V [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain M [auth A] SDF format, chain R [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B]	AA [auth D], M [auth A], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain M [auth A] Focus chain R [auth B] Interactions & Density Focus chain AA [auth D] Focus chain M [auth A] Focus chain R [auth B]