SMTL ID : 1fzg.1

CRYSTAL STRUCTURE OF FRAGMENT D FROM HUMAN FIBRINOGEN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x GLY- HIS- ARG- PRO: FIBRINOGEN(Non-covalent)

GLY-HIS-ARG-PRO.1: 12 residues within 4Å: Chain C: D.211, D.214, F.217, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.218, C:F.235 Hydrogen bonds: C:D.214, C:Q.242, C:K.251, C:K.251, C:C.252, C:H.253, C:D.277 Salt bridges: C:D.243 pi-Cation interactions: C:Y.276 GLY-HIS-ARG-PRO.2: 12 residues within 4Å: Chain F: F.208, D.210, D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:T.218, F:F.235 Hydrogen bonds: F:Q.242, F:K.251, F:C.252, F:H.253, F:D.277 Water bridges: F:D.243, F:D.243 Salt bridges: F:D.243 pi-Cation interactions: F:Y.276 GLY-HIS-ARG-PRO.3: 13 residues within 4Å: Chain B: L.227, N.231, M.234, T.235, W.252, E.264, D.265, R.273, C.274, H.275, D.299, M.305 Ligands: NAG-NAG.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.252 Hydrogen bonds: B:R.273, B:R.273, B:C.274, B:H.275, B:D.299 Water bridges: B:D.265, B:D.265 Salt bridges: B:E.264, B:D.265 GLY-HIS-ARG-PRO.4: 13 residues within 4Å: Chain E: L.227, N.231, M.234, T.235, W.252, E.264, D.265, R.273, C.274, H.275, T.298, D.299, M.305 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:L.227, E:T.235, E:W.252 Hydrogen bonds: E:E.264, E:R.273, E:R.273, E:C.274, E:H.275, E:H.275 Water bridges: E:N.231 Salt bridges: E:D.265

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 5 residues within 4Å: Chain B: L.227, M.228, N.231 Ligands: GLY-HIS-ARG-PRO.3, GLY-HIS-ARG-PRO.3 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain E: M.228, E.230, N.231 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain B: D.248, D.250, W.252, K.259 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.248, B:D.250, B:W.252, H2O.1 CA.8: 3 residues within 4Å: Chain B: D.128, G.130 Chain C: E.45 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.45, B:D.128 CA.9: 4 residues within 4Å: Chain C: D.231, D.233, F.235, G.237 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.231, C:D.233, C:F.235, C:G.237, H2O.2 CA.10: 5 residues within 4Å: Chain C: D.207, G.209, D.211, D.214, K.215 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.207, C:D.211, C:D.214, C:D.214, H2O.2 CA.11: 3 residues within 4Å: Chain E: D.248, D.250, W.252 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.248, E:D.248, E:D.250, E:W.252, H2O.3 CA.12: 3 residues within 4Å: Chain E: D.128, G.130 Chain F: E.45 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.128, E:D.128, E:G.130, F:E.45, H2O.4 CA.13: 4 residues within 4Å: Chain F: D.231, D.233, F.235, G.237 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.231, F:D.233, F:F.235, F:G.237, H2O.4 CA.14: 4 residues within 4Å: Chain F: D.207, G.209, D.211, D.214 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.207, F:D.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Everse, S.J. et al., Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide. Biochemistry (1999)

Release Date

1999-06-08

Peptides

FIBRINOGEN: AD
FIBRINOGEN: BE
FIBRINOGEN: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

FIBRINOGEN

FIBRINOGEN

FIBRINOGEN

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