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SMTL ID : 1hlt.1

THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

0G6.1:	18 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 16 PLIP interactions: 16 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.226, B:G.228, B:G.228, B:G.230 Salt bridges: B:D.199
0G6.2:	19 residues within 4Å: Chain D: H.43, Y.47, W.50, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.47, D:W.50, D:I.179, D:W.227 Hydrogen bonds: D:A.200, D:G.203, D:D.204, D:S.205, D:S.226, D:W.227, D:G.228, D:G.228, D:G.230 Salt bridges: D:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Mathews, I.I. et al., Structure of a nonadecapeptide of the fifth EGF domain of thrombomodulin complexed with thrombin. Biochemistry (1994)

Release Date

1994-12-20

Peptides

ALPHA-THROMBIN (SMALL SUBUNIT): AC
ALPHA-THROMBIN (LARGE SUBUNIT): BD
Thrombomodulin: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
J

B
H

D
K

E
R

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

ALPHA-THROMBIN (SMALL SUBUNIT)

Toggle Identical (AC)

ALPHA-THROMBIN (LARGE SUBUNIT)

Toggle Identical (BD)

Thrombomodulin

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