3N2C

Crystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline

Structural Biology Knowledgebase: 3N2C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3N2C

Classification: HYDROLASE

Total Structure Weight: 725093.06

Macromolecule Entities
Molecule Chains Length Organism Details
PROLIDASE A, B, C..., D, E, F, G, H, I, J, K, L, M, N, O, PA, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P 423 Unidentified Gene Name(s): Bcep18194_B2354

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

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P 1-[(R)-hydroxy(methyl)phosphoryl]-L-proline
C6 H12 N O4 P
IIXOSEXCIQDQTO-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LWY N/A in BindingDB
N/A in BindingMoad
Ki: 7500 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.220
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 113.19 α = 81.32
b = 108.04 β = 80.47
c = 170.77 γ = 73.76

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-05-17
  • Released Date: 2010-06-02
  • Deposition author(s): Patskovsky, Y., Xu, C., Sauder, J.M., Burley, S.K., Raushel, F.M., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
  • Previous versions: 3LWY

Revision History

  • 2012-10-10
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4