1DVA

Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA

Structural Biology Knowledgebase: 1DVA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 1DVA

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 85049.58

Macromolecule Entities
Molecule Chains Length Organism Details
DES-GLA FACTOR VIIA (HEAVY CHAIN) H, I 254 Homo sapiens EC#: 3.4.21.21 IUBMB
Gene Name(s): F7 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DES-GLA FACTOR VIIA (LIGHT CHAIN) L, M 101 Homo sapiens EC#: 3.4.21.21 IUBMB
Gene Name(s): F7 Gene View
PEPTIDE E-76 X, Y 20 synthetic

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0Z6
Query on 0Z6

H, I 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

M ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

L BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

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

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

M BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE (Synonym)
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAC
Query on CAC

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

H, I, L, M CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000369
Query on PRD_000369
H, I D-Phe-Phe-Arg Chloromethylketone Peptide-like /
Inhibitor
Ligand Explorer
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
X, Y NON-POLYMER C2 H4 O --
NH2
Query on NH2
X, Y NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.225
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 70.49 α = 90.00
b = 55.26 β = 99.48
c = 111.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-20
  • Released Date: 2000-05-12
  • Deposition author(s): Eigenbrot, C., Ultsch, M.H.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 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: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 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: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description