1DX5

Crystal structure of the thrombin-thrombomodulin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 1DX5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 189363.34

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN LIGHT CHAIN A, B, C, D 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN INHIBITOR GLU-GLY-ARG-0QE E, F, G, H 4 Synthetic construct
THROMBOMODULIN I, J, K, L 118 Homo sapiens Fragment: EGF-LIKE DOMAINS 4 - 6
Mutation: N364D, R456G, H457Q
Details: ENZYMATICALLY DEGLYCOSYLATED (PNGASE F)
Gene Name(s): THBD Gene View THRM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN HEAVY CHAIN M, N, O, P 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Mutation: T60II
Gene Name(s): F2 Gene View

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

M, N, O, P N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

H, I, J, K, L FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

I, J, K, L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

I, J, K, L, M, N, O, P SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
AR7
Query on AR7
E, F, G, H peptide-like C6 H17 N4 O2 ARG
0QE
Query on 0QE
E, F, G, H NON-POLYMER C H3 Cl --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.200
  • Space Group: H 3

Unit Cell:

Length (Å) Angle (°)
a = 214.40 α = 90.00
b = 214.40 β = 90.00
c = 131.41 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-20
  • Released Date: 2000-04-10
  • Deposition author(s): Fuentes-Prior, P., Iwanaga, Y., Huber, R., Pagila, R., Rumennik, G., Seto, M., Morser, J., Light, D.R., Bode, W.

Revision History

  • 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • 2016-12-21
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy