SMTL ID : 1rf1.1 (1 other biounit)

Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GLY- HIS- ARG- PRO: GHRP peptide(Non-covalent)

GLY-HIS-ARG-PRO.1: 13 residues within 4Å: Chain C: F.200, D.202, D.206, T.210, F.227, Q.234, D.235, K.243, C.244, H.245, Y.268, D.269, R.280 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.210, C:F.227, C:F.227 Hydrogen bonds: C:Q.234, C:K.243, C:K.243, C:C.244, C:H.245, C:D.269 Salt bridges: C:D.235 pi-Cation interactions: C:Y.268 GLY-HIS-ARG-PRO.2: 15 residues within 4Å: Chain B: L.212, N.216, M.219, T.220, W.237, E.249, D.250, R.258, C.259, H.260, T.283, D.284, M.290 Ligands: NAG-NAG-FUC.3, NAG-NAG-FUC.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.212, B:T.220, B:W.237 Hydrogen bonds: B:R.258, B:R.258, B:C.259, B:H.260, B:T.283, B:T.283, B:D.284 Water bridges: B:D.284 Salt bridges: B:E.249, B:D.250, B:R.258

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 4 residues within 4Å: Chain B: M.213, N.216 Ligands: GLY-HIS-ARG-PRO.2, GLY-HIS-ARG-PRO.2 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain B: D.233, D.235, W.237 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.233, B:D.233, B:D.235, B:W.237, H2O.1 CA.5: 5 residues within 4Å: Chain C: D.223, D.225, F.227, E.228, G.229 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.223, C:D.223, C:D.225, C:F.227, C:G.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kostelansky, M.S. et al., Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization. Biochemistry (2004)

Release Date

2004-03-16

Peptides

Fibrinogen alpha/alpha-E chain: A
Fibrinogen beta chain: B
Fibrinogen gamma chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fibrinogen alpha/alpha-E chain

Fibrinogen beta chain

Fibrinogen gamma chain

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