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SMTL ID : 2zfq.1

Exploring thrombin S3 pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	3 residues within 4Å: Chain B: K.174, D.175, T.177 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.174, B:T.177
NA.2:	2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.238

1 x 45U: (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentyloxy)ethanoyl)pyrrolidine-2-carboxamide(Non-covalent)

45U.3:

16 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

13 PLIP interactions:

13 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:V.225, B:W.227, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:S.226, B:G.228
Water bridges: B:W.227, B:D.232, B:Y.240

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4:

3 residues within 4Å:

Chain B: S.176, G.235, K.236

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:S.176, B:K.236, B:K.236

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

2 residues within 4Å:

Chain B: L.46, N.53

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Brandt, T. et al., Exploring thrombin S3 pocket. To be Published

Release Date

2009-01-13

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Hirudin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

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

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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

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