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

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GLY- PRO- ARG- VAL: GLY-PRO-ARG-VAL-VAL-GLU peptide(Non-covalent)

GLY-PRO-ARG-VAL.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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.227, C:Y.268 Hydrogen bonds: C:Q.234, C:K.243, C:C.244, C:H.245, C:D.269 Salt bridges: C:D.235 pi-Cation interactions: C:Y.268 GLY-PRO-ARG-VAL.2: 13 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 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.212, B:W.237 Hydrogen bonds: B:R.258, B:C.259, B:H.260, B:D.284 Salt bridges: B:E.249, B:D.250

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: 3 residues within 4Å: Chain B: M.213, E.215, N.216 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 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.233, B:D.233, B:D.235, B:W.237 CA.5: 4 residues within 4Å: Chain C: D.223, D.225, F.227, 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

Betts, L. et al., The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE. THROMB.HAEMOST. (2006)

Release Date

2006-07-04

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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