3GVK

Crystal structure of endo-neuraminidase NF mutant

Structural Biology Knowledgebase: 3GVK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.265

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GVK

Classification: HYDROLASE

Total Structure Weight: 230649.59

Macromolecule Entities
Molecule Chains Length Organism Details
Endo-N-acetylneuraminidase A, B, C 670 Enterobacteria phage k1f EC#: 3.2.1.129 IUBMB
Fragment: residues 246-910
Mutation: H350A
Gene Name(s):

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

A, B, C 5-N-ACETYL-BETA-D-NEURAMINIC ACID
BETA-SIALIC ACID (Synonym)
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIA
Query on SIA

A, B, C O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.265
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 90.40 α = 90.00
b = 153.70 β = 90.00
c = 157.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-31
  • Released Date: 2010-03-02
  • Deposition author(s): Schulz, E.C., Dickmanns, A., Ficner, R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4