2YA6

CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANA (TIGR4) IN COMPLEX WITH DANA

Structural Biology Knowledgebase: 2YA6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YA6

Classification: HYDROLASE

Total Structure Weight: 111578.15

Macromolecule Entities
Molecule Chains Length Organism Details
NEURAMINIDASE A A, B 493 Streptococcus pneumoniae EC#: 3.2.1.18 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 280-754
Mutation: E440K, N584D
Details: THE SEQUENCE NUMBERING ABOVE CORRESPONDS TO THE CLOSEST UNIPROT SEQUENCE MATCH UNP B2DJD9. THE SEQUENCE NUMBERING FOR THE ENTRY SHOULD BE 303-777
Gene Name(s): nanA

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

A, B 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAN N/A in BindingDB
Ki: 2000 nM  BindingMOAD
Ki: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 164.86 α = 90.00
b = 48.83 β = 104.13
c = 125.38 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-18
  • Released Date: 2011-04-27
  • Deposition author(s): Gut, H., Xu, G., Taylor, G.L., Walsh, M.A.

Revision History

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