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

Crystal Structure of Human Fibrinogen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GLY- PRO- ARG- PRO: A knob(Non-covalent)

GLY-PRO-ARG-PRO.1: 12 residues within 4Å: Chain C: F.295, D.297, D.301, F.322, Q.329, D.330, K.338, C.339, H.340, Y.363, D.364, R.375 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.322, C:F.322 Hydrogen bonds: C:Q.329, C:K.338, C:K.338, C:C.339, C:H.340, C:D.364, C:D.364 Salt bridges: C:D.330, C:K.338 GLY-PRO-ARG-PRO.2: 12 residues within 4Å: Chain F: F.295, D.297, D.301, T.305, F.322, Q.329, D.330, K.338, C.339, H.340, Y.363, D.364 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:F.295, F:T.305, F:F.322, F:K.338 Hydrogen bonds: F:Q.329, F:K.338, F:C.339, F:H.340, F:D.364, F:D.364 Salt bridges: F:D.330, F:K.338 pi-Cation interactions: F:Y.363

2 x GLY- HIS- ARG- PRO: B knob(Non-covalent)

GLY-HIS-ARG-PRO.3: 14 residues within 4Å: Chain B: L.360, N.364, M.367, T.368, W.385, E.397, D.398, R.406, C.407, H.408, T.431, D.432, M.438 Ligands: NAG-NAG-BMA-MAN-MAN.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.360, B:T.368, B:W.385 Hydrogen bonds: B:R.406, B:R.406, B:C.407, B:H.408, B:D.432 Salt bridges: B:E.397, B:D.398, B:R.406, B:D.432 GLY-HIS-ARG-PRO.4: 14 residues within 4Å: Chain E: L.360, N.364, M.367, T.368, W.385, E.397, D.398, R.406, C.407, H.408, T.431, D.432, M.438 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG-GAL-SIA.6 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.360 Hydrogen bonds: E:R.406, E:C.407, E:H.408, E:T.431, E:T.431, E:D.432 Salt bridges: E:D.398, E:R.406, E:D.432

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain B: M.361, N.364 Ligands: GLY-HIS-ARG-PRO.3, GLY-HIS-ARG-PRO.3 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN- NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG-GAL-SIA.6: 5 residues within 4Å: Chain E: M.361, N.364, W.424 Ligands: GLY-HIS-ARG-PRO.4, GLY-HIS-ARG-PRO.4 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.7: 4 residues within 4Å: Chain F: Q.49, N.52, K.53, E.56 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain B: D.381, D.383, W.385 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.381, B:D.381, B:D.383, B:W.385 CA.9: 5 residues within 4Å: Chain C: D.318, D.320, F.322, E.323, G.324 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.318, C:D.318, C:D.320, C:F.322, C:G.324 CA.10: 3 residues within 4Å: Chain E: D.381, D.383, W.385 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.381, E:D.381, E:D.383, E:W.385 CA.11: 4 residues within 4Å: Chain F: D.318, D.320, F.322, G.324 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.318, F:D.318, F:D.320, F:F.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kollman, J.M. et al., Crystal structure of human fibrinogen. Biochemistry (2009)

Release Date

2009-05-19

Peptides

Fibrinogen alpha chain: AD
Fibrinogen beta chain: BE
Fibrinogen gamma chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

D
J

B
H

E
K

C
I

F
L

Fibrinogen alpha chain

Fibrinogen beta chain

Fibrinogen gamma chain

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