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

Crystal structure of recombinant gamma N308K fibrinogen fragment D with the peptide ligand Gly-Pro-Arg-Pro-amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GLY- PRO- ARG- PRO: Peptide Ligand Gly-Pro-Arg-Pro-amide(Non-covalent)

GLY-PRO-ARG-PRO.1: 12 residues within 4Å: Chain C: F.200, D.202, D.206, F.227, Q.234, D.235, K.243, C.244, H.245, Y.268, D.269, R.280 10 PLIP interactions: 10 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 Salt bridges: C:D.235, C:K.243 pi-Cation interactions: C:Y.268 GLY-PRO-ARG-PRO.2: 12 residues within 4Å: Chain B: L.212, M.219, W.237, E.249, D.250, R.258, C.259, H.260, T.283, D.284, M.290 Ligands: NAG-NAG-FUC.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.212 Hydrogen bonds: B:R.258, B:R.258, B:C.259, B:H.260, B:T.283, B:T.283, B:D.284 Salt bridges: B:E.249, B:D.250, B:R.258, B:D.284

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(Non-covalent)

NAG-NAG-FUC.3: 4 residues within 4Å: Chain B: L.212, M.213, N.216 Ligands: GLY-PRO-ARG-PRO.2 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.212

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain B: D.233, D.235, W.237 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.233, B:W.237, H2O.1 CA.5: 5 residues within 4Å: Chain C: D.223, D.225, F.227, E.228, G.229 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:F.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowley, S.R. et al., Impaired protofibril formation in fibrinogen gammaN308K is due to altered D:D and "A:a" interactions. Biochemistry (2009)

Release Date

2009-08-18

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

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