1NE7 | pdb_00001ne7

HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.217 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

Literature

Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study.

Arreola, R., Valderrama, B., Morante, M.L., Horjales, E.

(2003) FEBS Lett 551: 63-70

  • DOI: https://doi.org/10.1016/s0014-5793(03)00896-2
  • Primary Citation Related Structures: 
    1NE7

  • PubMed Abstract: 

    Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium. Here we describe the existence of two mammalian glucosamine-6-phosphate deaminase enzymes. We present the crystallographic structure of one of them, the long human glucosamine-6-phosphate deaminase, at 1.75 A resolution. Crystals belong to the space group P2(1)2(1)2(1) and present a whole hexamer in the asymmetric unit. The active-site lid (residues 162-182) presented significant structural differences among monomers. Interestingly the region with the largest differences, when compared with the Escherichia coli homologue, was found to be close to the active site. These structural differences can be related to the kinetic and allosteric properties of both mammalian enzymes.

    • Organizational Affiliation: 
    • Instituto de Biotecnología, Universidad Nacional Autónoma de México, PO Box 510-3, Cuernavaca, 62250 Morelos, Mexico. arreola@ibt.unam.mx

Macromolecule Content 

  • Total Structure Weight: 202.38 kDa 
  • Atom Count: 16,013 
  • Modeled Residue Count: 1,651 
  • Deposited Residue Count: 1,734 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucosamine-6-phosphate isomerase
A, B, C, D, E
A, B, C, D, E, F
289Homo sapiensMutation(s): 0 
Gene Names: GNPI OR HLN OR KIAA0060
EC: 3.5.99.6
UniProt & NIH Common Fund Data Resources
Find proteins for P46926 (Homo sapiens)
Explore P46926 
Go to UniProtKB:  P46926
PHAROS:  P46926
GTEx:  ENSG00000113552 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46926
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G92130SN
GlyCosmos: G92130SN

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16G

Query on 16G


Download:Ideal Coordinates CCD File
CA [auth F]
M [auth A]
P [auth B]
S [auth C]
W [auth D]
CA [auth F],
M [auth A],
P [auth B],
S [auth C],
W [auth D],
Z [auth E]
2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
C8 H16 N O9 P
BRGMHAYQAZFZDJ-PVFLNQBWSA-N
AGP

Query on AGP


Download:Ideal Coordinates CCD File
BA [auth E]
EA [auth F]
O [auth A]
R [auth B]
V [auth C]
BA [auth E],
EA [auth F],
O [auth A],
R [auth B],
V [auth C],
Y [auth D]
2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
C6 H16 N O8 P
LBNVXZROMBUNNQ-SLPGGIOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
AA [auth E]
DA [auth F]
N [auth A]
Q [auth B]
T [auth C]
AA [auth E],
DA [auth F],
N [auth A],
Q [auth B],
T [auth C],
U [auth C],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.217 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.877α = 90
b = 110.892β = 90
c = 180.881γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-10-14
    Changes: Structure summary
  • Version 2.2: 2023-08-16
    Changes: Advisory, Data collection, Database references, Refinement description