6YHG

Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)

• PDB DOI: https://doi.org/10.2210/pdb6YHG/pdb

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


• Deposited: 2020-03-29 Released: 2021-04-07 
• Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Collins, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.145 
• R-Value Work: 0.123 
• R-Value Observed: 0.124 

Starting Model: experimental

Literature

Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)

Sandner, A., 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: 36.3 kDa 
• Atom Count: 2,936 
• Modelled Residue Count: 294 
• Deposited Residue Count: 307 
• 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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00734-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DPN	I [auth H]	D-PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-MRVPVSSYSA-N
SZ4	K [auth H]	1-(3-methoxyphenyl)methanamine C8 H11 N O GRRIMVWABNHKBX-UHFFFAOYSA-N
PRO	J [auth H]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
PO4	D [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth H], F [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: 1.33 Å
• R-Value Free: 0.145 
• R-Value Work: 0.123 
• R-Value Observed: 0.124 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.25	α = 90
b = 71.251	β = 100.61
c = 72.742	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Sandner, A., Heine, A., Klebe, G., Collins, C.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary