4NDZ

Structure of Maltose Binding Protein fusion to 2-O-Sulfotransferase with bound heptasaccharide and PAP

Structural Biology Knowledgebase: 4NDZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4NDZ

Classification: TRANSPORT PROTEIN / TRANSFERASE

Total Structure Weight: 458291.07

Macromolecule Entities
Molecule Chains Length Organism Details
Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 fusion A, B, C..., D, E, FA, B, C, D, E, F 658 Escherichia coli Gallus gallus EC#: 2.8.2 IUBMB
Mutation: E359A, K362A, D363A, R367N
Gene Name(s): malE b4034 JW3994 HS2ST1 Gene View HS2ST

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A3P
Query on A3P

A, B, C, D, E, F ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GNS
Query on GNS

A, B, D, E, F N-SULFO-ALPHA-D-GLUCOSAMINE
C6 H13 N O8 S
PRDZVHCOEWJPOB-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

A, B, D, E, F 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IDR
Query on IDR

A, B, D, E, F L-IDURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-VCSGLWQLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BDP
Query on BDP

A, B, D, E, F BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

B, C, D, E, F ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NPO
Query on NPO

A, B, D, E P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.176
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 155.72 α = 90.00
b = 170.69 β = 90.00
c = 183.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-28
  • Released Date: 2014-03-19
  • Deposition author(s): Liu, C., Sheng, J., Krahn, J.M., Perera, L., Xu, Y., Hsieh, P., Liu, J., Pedersen, L.C.

Revision History

No revisions since initial release