SMTL ID : 1n86.1

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GLY- PRO- ARG: fibrin alpha chain peptide ligand fragment Gly-Pro-Arg(Non-covalent)

GLY-PRO-ARG.1: 12 residues within 4Å: Chain C: F.208, D.210, D.214, T.218, F.235, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.235 Hydrogen bonds: C:Q.242, C:H.253, C:D.277 Salt bridges: C:D.243, C:K.251 pi-Cation interactions: C:Y.276 GLY-PRO-ARG.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 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:F.208, F:F.235, F:K.251 Hydrogen bonds: F:Q.242, F:H.253, F:D.277 Salt bridges: F:D.243, F:K.251 pi-Cation interactions: F:F.235, F:Y.276

2 x GLY- HIS- ARG- PRO: fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys(Non-covalent)

GLY-HIS-ARG-PRO.3: 13 residues within 4Å: Chain B: L.227, N.231, M.234, W.252, E.264, D.265, R.273, C.274, H.275, T.298, D.299, M.305 Ligands: NDG.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.227, B:W.252, B:W.252 Hydrogen bonds: B:N.231, B:R.273, B:H.275, B:D.299 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, W.252, E.264, D.265, R.273, C.274, H.275, T.298, D.299, M.305 Ligands: NDG.9 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.227, E:W.252 Hydrogen bonds: E:N.231, E:R.273, E:H.275, E:D.299 Salt bridges: E:E.264, E:D.265

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

NDG.5: 6 residues within 4Å: Chain B: L.227, M.228, N.231 Ligands: GLY-HIS-ARG-PRO.3, GLY-HIS-ARG-PRO.3, NDG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.228, B:N.231 NDG.9: 4 residues within 4Å: Chain E: M.228, N.231 Ligands: GLY-HIS-ARG-PRO.4, NDG.13 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:M.228 Hydrogen bonds: E:N.231 NDG.12: 2 residues within 4Å: Ligands: NDG.5, MAN.6 No protein-ligand interaction detected (PLIP) NDG.13: 1 residues within 4Å: Ligands: NDG.9 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.6: 1 residues within 4Å: Ligands: NDG.12 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain B: D.248, D.250, W.252 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.248, B:D.248, B:D.250, B:W.252 CA.8: 5 residues within 4Å: Chain C: D.231, D.233, F.235, E.236, G.237 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.231, C:D.231, C:D.233, C:F.235, C:G.237 CA.10: 3 residues within 4Å: Chain E: D.248, D.250, W.252 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.248, E:D.248, E:D.250, E:W.252 CA.11: 5 residues within 4Å: Chain F: D.231, D.233, F.235, E.236, G.237 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.231, F:D.231, F:D.233, F:F.235, F:G.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface. Biochemistry (2002)

Release Date

2003-01-07

Peptides

Fibrin alpha/alpha-E chain: AD
Fibrin beta chain: BE
Fibrin gamma chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Fibrin alpha/alpha-E chain

Fibrin beta chain

Fibrin gamma chain

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