4OCJ

N-acetylhexosamine 1-phosphate kinase in complex with GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb4OCJ/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium longum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-09 Released: 2014-05-14 
• Deposition Author(s): Li, T.L., Wang, K.C., Lyu, S.Y., Liu, Y.C., Chang, C.Y., Wu, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.91 kDa 
• Atom Count: 3,325 
• Modelled Residue Count: 355 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylhexosamine 1-phosphate kinase	A	379	Bifidobacterium longum	Mutation(s): 0  Gene Names: mdsC, BN57_1851 EC: 2.7.1.162
UniProt
Find proteins for E8MF12 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)) Explore E8MF12  Go to UniProtKB:  E8MF12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	B [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
NDG	Binding MOAD:  4OCJ	Kd: 2.04e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.367	α = 90
b = 79.51	β = 90
c = 98.122	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Li, T.L., Wang, K.C., Lyu, S.Y., Liu, Y.C., Chang, C.Y., Wu, C.J.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary