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SMTL ID : 3bf6.1

Thrombin:suramin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-oligomer

Ligands

1 x PHE- PRO- ARG: PHE-PRO-ARG(Non-covalent)

PHE-PRO-ARG.1:

19 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, G.238

19 PLIP interactions:

19 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:I.179, B:W.227, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:D.204, B:S.205, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:Y.240
Salt bridges: B:D.199

1 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID(Non-covalent)

SVR.2:

12 residues within 4Å:

Chain B: H.87, P.88, R.89, R.98, K.248, W.249, K.252, V.253, D.255, Q.256, G.258, E.259

25 PLIP interactions:

25 interactions with chain B

Hydrophobic interactions: B:K.252, B:K.252, B:V.253, B:Q.256, B:E.259
Hydrogen bonds: B:K.252, B:D.255, B:E.259, B:E.259
Water bridges: B:H.87, B:R.98, B:K.248, B:W.249, B:K.252, B:K.252, B:D.255, B:D.255, B:Q.256
Salt bridges: B:H.87, B:R.89, B:R.89, B:R.98, B:K.248, B:K.248, B:K.252

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Lima, L.M. et al., Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases. Biochim.Biophys.Acta (2009)

Release Date

2007-12-25

Peptides

Thrombin, LIGHT CHAIN: A
Thrombin, HEAVY CHAIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

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

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