SMTL ID : 1ppc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x MID: 1-[N-(NAPHTHALEN-2-YLSULFONYL)GLYCYL-4-CARBAMIMIDOYL-D-PHENYLALANYL]PIPERIDINE(Non-covalent)

MID.1: 16 residues within 4Å: Chain A: H.40, S.78, N.79, L.81, D.171, S.172, C.173, Q.174, S.177, S.192, W.193, G.194, S.195, G.196, C.197, G.204 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.81, A:W.193 Hydrogen bonds: A:D.171, A:S.172, A:S.177, A:G.194, A:G.194, A:G.196, A:G.196 Water bridges: A:D.171, A:V.205

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.52, N.54, V.57, E.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H2O.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bode, W. et al., 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-tetrahydr 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. Eur.J.Biochem. (1990)

Release Date

1994-01-31

Peptides

TRYPSIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

TRYPSIN

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