SMTL ID : 1m1j.1

Crystal structure of native chicken fibrinogen with two different bound ligands

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

GLY-PRO-ARG-PRO.1: 12 residues within 4Å: Chain C: F.295, D.301, T.305, F.322, Q.329, D.330, R.338, C.339, H.340, Y.363, D.364, R.375 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.295, C:F.322 Hydrogen bonds: C:Q.329, C:R.338, C:H.340, C:D.364 Salt bridges: C:D.330, C:R.338 pi-Cation interactions: C:Y.363 GLY-PRO-ARG-PRO.2: 12 residues within 4Å: Chain F: F.295, D.301, T.305, F.322, Q.329, D.330, R.338, C.339, H.340, Y.363, D.364, R.375 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:F.295, F:F.322, F:R.338 Hydrogen bonds: F:Q.329, F:R.338, F:H.340, F:D.364 Salt bridges: F:D.330, F:R.338 pi-Cation interactions: F:Y.363

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

GLY-HIS-ARG-PRO.3: 14 residues within 4Å: Chain B: L.364, N.368, M.371, T.372, W.389, E.401, D.402, R.410, C.411, H.412, T.435, D.436, M.442 Ligands: NDG.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.364, B:T.372, B:W.389, B:W.389, B:R.410 Hydrogen bonds: B:R.410, B:R.410, B:H.412, B:D.436 Salt bridges: B:E.401, B:D.402, B:R.410 GLY-HIS-ARG-PRO.4: 15 residues within 4Å: Chain E: L.364, N.368, M.371, T.372, W.389, E.401, D.402, R.410, C.411, H.412, T.435, D.436, M.442, S.447 Ligands: NDG.10 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.364, E:T.372, E:W.389, E:W.389 Hydrogen bonds: E:R.410, E:R.410, E:H.412, E:T.435, E:S.447, E:S.447 Salt bridges: E:E.401, E:D.402, E:R.410

5 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)(Non-functional Binders)

NDG.5: 5 residues within 4Å: Chain B: Y.365, N.368 Ligands: GLY-HIS-ARG-PRO.3, GLY-HIS-ARG-PRO.3, NAG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.368 NDG.7: 2 residues within 4Å: Chain C: N.52, S.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.52, C:S.56, C:S.56 NDG.10: 5 residues within 4Å: Chain E: Y.365, N.368 Ligands: GLY-HIS-ARG-PRO.4, GLY-HIS-ARG-PRO.4, NDG.16 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.368 NDG.12: 4 residues within 4Å: Chain F: N.52, G.55, S.56 Ligands: NAG.13 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.52, F:N.52, F:S.56 NDG.16: 1 residues within 4Å: Ligands: NDG.10 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain B: D.385, D.387, W.389 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.385, B:D.385, B:D.387, B:W.389 CA.9: 4 residues within 4Å: Chain C: D.318, D.320, F.322, 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.11: 3 residues within 4Å: Chain E: D.385, D.387, W.389 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.385, E:D.385, E:D.387, E:W.389 CA.14: 4 residues within 4Å: Chain F: D.318, D.320, F.322, G.324 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.318, F:D.318, F:D.320, F:F.322, F:G.324

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Ligands: NDG.12 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Ligands: NDG.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Crystal Structure of Native Chicken Fibrinogen at 2.7 A Resolution. Biochemistry (2001)

Release Date

2002-06-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Fibrinogen alpha subunit

Fibrinogen beta chain

Fibrinogen gamma chain