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SMTL ID : 4e7r.2 (1 other biounit)

Thrombin in complex with 3-amidinophenylalanine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1:

1 residues within 4Å:

Chain B: N.53

No protein-ligand interaction detected (PLIP)

1 x 0NW: 3-[(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-{[(2',4'-dichlorobiphenyl-3-yl)sulfonyl]amino}-3-oxopropyl]benzenecarboximidamide(Non-covalent)

0NW.2:

18 residues within 4Å:

Chain B: H.43, Y.47, W.50, N.95, L.96, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238

10 PLIP interactions:

10 interactions with chain B

Hydrophobic interactions: B:Y.47, B:L.96, B:V.225, B:W.227
Hydrogen bonds: B:H.43, B:D.199, B:W.227, B:G.228, B:G.230
Water bridges: B:R.233

2 x NA: SODIUM ION(Non-functional Binders)

NA.3:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177
NA.4:	3 residues within 4Å: Chain B: Y.190, R.233, K.236 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.235, B:K.236, B:K.236 Water bridges: B:D.234, B:G.238

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5:

5 residues within 4Å:

Chain B: R.89, N.91, D.97, R.98, R.180

7 PLIP interactions:

7 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97, B:R.180
Water bridges: B:N.184
Salt bridges: B:R.89, B:R.98

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6:

6 residues within 4Å:

Chain B: I.167, V.168, R.170, C.173, F.186, C.187

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:R.170, B:R.170, B:C.187
Water bridges: B:H.242

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hammami, M. et al., New 3-amidinophenylalanine-derived inhibitors of matriptase. MEDCHEMCOMM (2012)

Release Date

2012-06-20

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
G

C
J

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

Hirudin variant-2

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