SMTL ID : 3h32.1

Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GLY- HIS- ARG- PRO- TYR: Fibrin B knob pentapeptide(Non-covalent)

GLY-HIS-ARG-PRO-TYR.1: 14 residues within 4Å: Chain B: L.360, E.363, N.364, M.367, T.368, W.385, E.397, R.406, C.407, H.408, T.431, D.432, M.438 Ligands: NAG-NAG-MAN-MAN-NAG-GAL-SIA-MAN.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.360, B:T.368, B:R.406 Hydrogen bonds: B:R.406, B:R.406, B:C.407, B:H.408, B:H.408 Salt bridges: B:E.397, B:D.398 GLY-HIS-ARG-PRO-TYR.2: 15 residues within 4Å: Chain E: L.360, E.363, N.364, M.367, T.368, W.385, E.397, D.398, R.406, C.407, H.408, T.431, D.432, M.438 Ligands: NAG-NAG-MAN-MAN-NAG-GAL-SIA-MAN.4 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:T.368, E:W.385, E:W.385, E:R.406 Hydrogen bonds: E:R.406, E:R.406, E:R.406, E:C.407, E:H.408, E:H.408 Salt bridges: E:E.397, E:D.398 pi-Cation interactions: E:R.406

2 x NAG- NAG- MAN- MAN- NAG- GAL- SIA- MAN: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-NAG-GAL-SIA-MAN.3: 6 residues within 4Å: Chain B: M.361, E.363, N.364, W.424 Ligands: GLY-HIS-ARG-PRO-TYR.1, GLY-HIS-ARG-PRO-TYR.1 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN-NAG-GAL-SIA-MAN.4: 5 residues within 4Å: Chain E: M.361, N.364, W.424 Ligands: GLY-HIS-ARG-PRO-TYR.2, GLY-HIS-ARG-PRO-TYR.2 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.424

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain B: D.381, D.383, W.385 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.381, B:D.383, B:W.385 CA.6: 6 residues within 4Å: Chain C: D.224, D.226, F.228, E.229, G.230, N.231 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.224, C:D.224, C:D.226, C:F.228, C:E.229 CA.7: 3 residues within 4Å: Chain E: D.381, D.383, W.385 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.381, E:D.383, E:D.383, E:W.385 CA.8: 3 residues within 4Å: Chain F: E.229, G.230, N.231 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandi, L. et al., Two families of synthetic peptides that enhance fibrin turbidity and delay fibrinolysis by different mechanisms. Biochemistry (2009)

Release Date

2009-07-28

Peptides

Fibrinogen alpha chain: AD
Fibrinogen beta chain: BE
Fibrinogen gamma chain, isoform gamma-A: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Fibrinogen alpha chain

Fibrinogen beta chain

Fibrinogen gamma chain, isoform gamma-A