PDBsum entry 1fze

Blood coagulation

PDB id: 1fze

Contents

Protein chains

81 a.a. *

309 a.a. *

303 a.a. *

Ligands

NAG ×4

Metals

_CA ×6

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Conformational changes in fragments d and double-D from human fibrin(ogen) upon binding the peptide ligand gly-His-Arg-Pro-Amide.
• Authors: S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle.
• Ref.: Biochemistry, 1999, 38, 2941-2946. [DOI no: 10.1021/bi982626w]
• PubMed id: 10074346

Abstract

The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand. Comparison of the structures has revealed a series of conformational changes that are brought about by the various knob-hole interactions. Of greatest interest is a moveable "flap" of two negatively charged amino acids (Glubeta397 and Aspbeta398) whose side chains are pinned back to the coiled coil with a calcium atom bridge until GHRPam occupies the beta-chain pocket. Additionally, in the absence of the peptide ligand GPRPam, GHRPam binds to the gamma-chain pocket, a new calcium-binding site being formed concomitantly.