6T3M

Thrombin in Complex with a D-Phe-Pro-p-phenol derivative

• PDB DOI: https://doi.org/10.2210/pdb6T3M/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2019-10-11 Released: 2020-11-18 
• Deposition Author(s): Ngo, K., Collins, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.158 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

Literature

Thrombin in Complex with a D-Phe-Pro-p-phenol derivative

Ngo, K., Collins, C., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.47 kDa 
• Atom Count: 2,712 
• Modelled Residue Count: 291 
• Deposited Residue Count: 306 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth L]	36	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B [auth H]	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MD8 (Subject of Investigation/LOI)	E [auth H], F [auth H]	(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide C21 H25 N3 O3 FQTMKKZTHOHYNU-MOPGFXCFSA-N
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	G [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	H, I [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	C [auth I]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.158 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.301	α = 90
b = 71.476	β = 100.619
c = 72.573	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Ngo, K., Collins, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description