1Y5U

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

Structural Biology Knowledgebase: 1Y5U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Y5U

Classification: Hydrolase

Total Structure Weight: 24271.35

Macromolecule Entities
Molecule Chains Length Organism Details
Trypsin, cationic T 223 Bos taurus EC#: 3.4.21.4 IUBMB
Mutation: N97E, L99Y
Gene Name(s):

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TL4
Query on TL4

T 2-O-{3-[AMINO(IMINO)METHYL]PHENYL}-5-O-{4- [AMINO(IMINO)METHYL]PHENYL}-1,4:3,6-DIANHYDRO- D-GLUCITOL
4:3, (Synonym)
C20 H22 N4 O4
DKBAWRNTUZFJKV-XMTFNYHQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

T DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

T SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

T GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

T IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

T CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TL4 N/A in BindingDB
Kd: 220 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.157
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.79 α = 90.00
b = 54.79 β = 90.00
c = 108.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-03
  • Released Date: 2005-12-13
  • Deposition author(s): Di Fenza, A., Heine, A., Klebe, G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update