› 1ppc

X-ray diffraction
1.8Å resolution

GEOMETRY OF BINDING OF THE BENZAMIDINE-AND ARGININE-BASED INHIBITORS N-ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P-AMIDINOPHENYLALANYL-PIPERIDINE (NAPAP) AND (2R,4R)-4-METHYL-1-[N-ALPHA-(3-METHYL-1,2,3,4-TETRAHYDRO-8-QUINOLINESULPHONYL)-L-ARGINYL]-2-PIPERIDINE CARBOXYLIC ACID (MQPA) TO HUMAN ALPHA-THROMBIN: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE NAPAP-TRYPSIN COMPLEX AND MODELING OF NAPAP-THROMBIN AND MQPA-THROMBIN

Released:
DOI: 10.2210/pdb1ppc/pdb
PDB entry 1ppc coloured by chain, front view.
PDB entry 1ppc coloured by chain, side view.
PDB entry 1ppc coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin.
Bode W, Turk D, Stürzebecher J
Eur J Biochem 193 175-82 (1990)
PMID: 2226434

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: Arg-|-, Lys-|-.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133319 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine protease 1 Chain: E
Molecule details ›
Chain: E
Length: 223 amino acids
Theoretical weight: 23.32 KDa
Source organism: Bos taurus
Expression system: Not provided
UniProt:
  • Canonical: P00760 (Residues: 24-246; Coverage: 97%)
Gene names: PRSS1, TRP1, TRY1, TRYP1
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

2 bound ligands:
Ligand MID 1 x MID
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 63.51Å b: 69.19Å c: 63.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.181 not available
Expression system: Not provided

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Citations

9 review citations

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs.
Böhm HJ. (1998)
8 more

14 mentions without citation

Assessment of programs for ligand binding affinity prediction.
Kim et al. (2008)
13 more