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SMTL ID : 1sfq.2 (1 other biounit)

Fast form of thrombin mutant R(77a)A bound to PPACK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.1:

20 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238

18 PLIP interactions:

18 interactions with chain B

Hydrophobic interactions: B:Y.47, B:L.96, B:I.179, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:E.229, B:G.230, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

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

NAG.2:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

No protein-ligand interaction detected (PLIP)

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

NA.3:

3 residues within 4Å:

Chain B: D.232, R.233, K.236

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:R.233, B:K.236
Water bridges: B:R.197, B:R.233, B:G.235

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pineda, A.O. et al., Molecular dissection of na+ binding to thrombin. J.Biol.Chem. (2004)

Release Date

2004-06-08

Peptides

thrombin: A
thrombin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

thrombin

thrombin

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