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SMTL ID : 2a45.1

Crystal structure of the complex between thrombin and the central "E" region of fibrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

hetero-2-2-2-2-2-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: C.28, H.43, C.44, W.50, N.95, L.96, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238

15 PLIP interactions:

15 interactions with chain B

Hydrophobic interactions: B:W.50, B:L.96, B:L.96, B:W.227, B:W.227
Hydrogen bonds: B:A.200, B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228
Salt bridges: B:D.199
pi-Stacking: B:W.227, B:W.227

0G6.3:

20 residues within 4Å:

Chain D: H.43, C.44, Y.47, W.50, 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
Ligands: PO4.4

16 PLIP interactions:

16 interactions with chain D

Hydrophobic interactions: D:H.43, D:Y.47, D:W.50, D:L.96, D:L.96, D:I.179, D:W.227, D:W.227
Hydrogen bonds: D:H.43, D:D.199, D:G.203, D:S.205, D:G.228, D:G.228
Salt bridges: D:E.202
pi-Stacking: D:W.227

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

PO4.2:	3 residues within 4Å: Chain B: L.27, E.202, G.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.202
PO4.4:	5 residues within 4Å: Chain D: L.27, C.28, C.44, K.52 Ligands: 0G6.3 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.27, D:C.44 Salt bridges: D:K.52

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pechik, I. et al., Structural basis for sequential cleavage of fibrinopeptides upon fibrin assembly. Biochemistry (2006)

Release Date

2006-05-02

Peptides

Thrombin light chain: AC
Thrombin heavy chain: BD
Fibrinogen alpha chain: EH
Fibrinogen beta chain: FI
Fibrinogen gamma chain: GJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

E
G

H
J

F
H

I
K

G
I

J
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Toggle Identical (AC)

Thrombin heavy chain

Toggle Identical (BD)

Fibrinogen alpha chain

Toggle Identical (EH)

Fibrinogen beta chain

Toggle Identical (FI)

Fibrinogen gamma chain

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