4UDG

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UHGB_MP
A, B, C, D, E
A, B, C, D, E, F
347uncultured organismMutation(s): 0 
EC: 2.4.1
UniProt
Find proteins for D9ZDQ9 (uncultured organism)
Explore D9ZDQ9 
Go to UniProtKB:  D9ZDQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9ZDQ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

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AA [auth E]
GA [auth F]
H [auth A]
N [auth B]
S [auth C]
AA [auth E],
GA [auth F],
H [auth A],
N [auth B],
S [auth C],
W [auth D]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
PO4
Query on PO4

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FA [auth F]
G [auth A]
M [auth B]
R [auth C]
V [auth D]
FA [auth F],
G [auth A],
M [auth B],
R [auth C],
V [auth D],
Z [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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BA [auth E]
HA [auth F]
I [auth A]
O [auth B]
P [auth B]
BA [auth E],
HA [auth F],
I [auth A],
O [auth B],
P [auth B],
T [auth C],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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DA [auth E],
EA [auth E],
JA [auth F],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

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CA [auth E]
IA [auth F]
J [auth A]
Q [auth B]
U [auth C]
CA [auth E],
IA [auth F],
J [auth A],
Q [auth B],
U [auth C],
Y [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.816α = 90
b = 140.912β = 90
c = 168.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary