4BAM

Thrombin in complex with inhibitor

Structural Biology Knowledgebase: 4BAM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BAM

Classification: HYDROLASE

Total Structure Weight: 36136.32

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN LIGHT CHAIN A 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN HEAVY CHAIN B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
HIRUDIN VARIANT-1 D 12 Hirudo medicinalis Fragment: RESIDUES 53-64
Details: SYNTHETIC C-TERMINAL PEPTIDE 53-64 (WITH SULFATO-TYR63)
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MM9
Query on MM9

B (2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [(2R)-2-cyclohexyl-2-[[2-(dimethylamino)- 2-oxidanylidene-ethyl]amino]ethanoyl]azetidine- 2-carboxamide
C24 H36 N6 O3
UBUHFANKPRTXGI-PZJWPPBQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MM9 N/A in BindingDB
Ki: 1.14 nM  BindingMOAD
Ki: 1.14 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
D L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.169
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.41 α = 90.00
b = 71.51 β = 100.34
c = 72.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-14
  • Released Date: 2013-01-16
  • Deposition author(s): Xue, Y., Musil, D.

Revision History

  • 2013-03-13
    Type: Binding sites and description | Details: SITE, REMARK 800
  • 2013-02-20
    Type: Citation | Details: JRNL