3Q58 | pdb_00003q58

Structure of N-acetylmannosamine-6-Phosphate Epimerase from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb3Q58/pdb

Classification: ISOMERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-27 Released: 2011-01-12
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Kudritska, M., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.174 (Depositor), 0.179 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 51.17 kDa
Atom Count: 3,837
Modeled Residue Count: 457
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmannosamine-6-phosphate 2-epimerase	A, B	229	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0 Gene Names: nanE, STY1166, t1791 EC: 5.1.3.9
UniProt
Find proteins for P60668 (Salmonella typhi) Explore P60668 Go to UniProtKB: P60668
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60668
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.174 (Depositor), 0.179 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33q58

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.153	α = 90
b = 139.31	β = 90
c = 38.423	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary