SMTL ID : 1ltj.2 (1 other biounit)

Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLY- PRO- ARG- PRO: Gly-Pro-Arg-Pro(Non-covalent)

GLY-PRO-ARG-PRO.1: 12 residues within 4Å: Chain C: F.200, D.206, T.210, F.227, Q.234, D.235, K.243, C.244, H.245, Y.268, D.269, R.280 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.200, C:F.227 Hydrogen bonds: C:Q.234, C:K.243, C:C.244, C:H.245, C:D.269 Water bridges: C:D.235, C:D.235 Salt bridges: C:D.235, C:K.243 pi-Cation interactions: C:Y.268

1 x GLY- HIS- ARG- PRO: Gly-His-Arg-Pro(Non-covalent)

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:T.220, B:W.237, B:R.258 Hydrogen bonds: B:R.258, B:C.259, B:H.260, B:T.283, B:T.283, B:D.284 Water bridges: B:D.250, B:D.250 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: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.233, B:D.235, B:W.237, H2O.3, H2O.4 CA.5: 4 residues within 4Å: Chain C: D.223, D.225, F.227, G.229 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.223, C:D.225, C:F.227, C:G.229, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kostelansky, M.S. et al., 2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and without Two Peptide Ligands: GHRP Binding to the "b" Site Disrupts Its Nearby Calcium-binding Site. Biochemistry (2002)

Release Date

2002-11-06

Peptides

Fibrinogen alpha/alpha-E chain: A
Fibrinogen Beta chain: B
Fibrinogen Gamma chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Fibrinogen alpha/alpha-E chain

Fibrinogen Beta chain

Fibrinogen Gamma chain

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