SMTL ID : 3bvh.2 (1 other biounit)

Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GLY- PRO- ARG- PRO: 4-mer peptide GPRP(Non-covalent)

GLY-PRO-ARG-PRO.1: 11 residues within 4Å: Chain C: F.194, D.200, T.204, F.221, Q.228, D.229, K.237, C.238, H.239, Y.262, A.263 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.194, C:T.204, C:F.221 Hydrogen bonds: C:Q.228, C:K.237, C:C.238, C:H.239, C:A.263 Salt bridges: C:D.229 pi-Cation interactions: C:Y.262 GLY-PRO-ARG-PRO.2: 14 residues within 4Å: Chain B: L.200, N.204, M.207, T.208, W.225, E.237, D.238, R.246, C.247, H.248, T.271, D.272, M.278 Ligands: NAG-NAG-FUC.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.200, B:T.208, B:W.225, B:R.246 Hydrogen bonds: B:R.246, B:C.247, B:H.248, B:D.272 Water bridges: B:D.238, B:D.238 Salt bridges: B:E.237, B:D.238, B:R.246

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(Post Translational Modification)

NAG-NAG-FUC.3: 4 residues within 4Å: Chain B: M.201, G.202, N.204 Ligands: GLY-PRO-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.221, D.223, W.225 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.221, B:D.221, B:D.223, B:W.225, H2O.1 CA.5: 4 residues within 4Å: Chain C: D.217, D.219, F.221, G.223 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.217, C:D.217, C:D.219, C:F.221, C:G.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowley, S.R. et al., Polymerization-defective fibrinogen variant gammaD364A binds knob "A" peptide mimic. Biochemistry (2008)

Release Date

2008-09-02

Peptides

Fibrinogen alpha 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 chain

Fibrinogen beta chain

Fibrinogen gamma chain

Related Entries With Identical Sequence