3RMM

Human Thrombin in complex with MI332

Structural Biology Knowledgebase: 3RMM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RMM

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36579.03

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin Light Chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Thrombin Heavy Chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-2 I 13 Hirudo medicinalis Fragment: residues in UNP 60-72

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

H GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
M32
Query on M32

H N-(benzylsulfonyl)-D-alanyl-N-[2-(aminomethyl)- 5-chlorobenzyl]-L-prolinamide
C23 H29 Cl N4 O4 S
MAUGNQAVJWFOOZ-IERDGZPVSA-N
Ligand Explorer
 
JSmol
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
PO4
Query on PO4

H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
M32 Ki: 2.2 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000964 H N-(BENZYLSULFONYL)-D-ALANYL-N-[2-(AMINOMETHYL)-5-CHLOROBENZYL]-L-PROLINAMIDE Peptide-like /
Thrombin inhibitor
Ligand Explorer
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.155
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.10 α = 90.00
b = 71.10 β = 100.40
c = 72.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-21
  • Released Date: 2012-04-25
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info