1DAN

Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor

Structural Biology Knowledgebase: 1DAN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1DAN

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 70003.98

Macromolecule Entities
Molecule Chains Length Organism Details
BLOOD COAGULATION FACTOR VIIA light chain L 152 Homo sapiens EC#: 3.4.21.21 IUBMB
Gene Name(s): F7 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
BLOOD COAGULATION FACTOR VIIA heavy chain H 254 Homo sapiens EC#: 3.4.21.21 IUBMB
Gene Name(s): F7 Gene View
SOLUBLE TISSUE FACTOR T 80 Homo sapiens Gene Name(s): F3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SOLUBLE TISSUE FACTOR U 121 Homo sapiens Gene Name(s): F3 Gene View

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0Z6
Query on 0Z6

H D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}- 1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide
FFRCK (Synonym)
C25 H36 Cl N6 O3
ZKHBINZTIMXMQW-CLAROIROSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

L BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

L ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAC
Query on CAC

H CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

H, L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000369 (PHE,DPN,AR7,0QE) H D-Phe-Phe-Arg Chloromethylketone Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CGU
Query on CGU
L L-PEPTIDE LINKING C6 H9 N O6 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.187
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.65 α = 90.00
b = 82.55 β = 90.00
c = 126.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-03-05
  • Released Date: 1997-09-04
  • Deposition author(s): Banner, D.W.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4