SMTL ID : 2hlo.2 (1 other biounit)

Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with Gly-hydroxyPro-Arg-Pro-amide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLY- HYP- ARG- PRO- NH2: GLY-HYP-ARG-PRO-AMIDE PEPTIDE LIGAND(Non-covalent)

GLY-HYP-ARG-PRO-NH2.1: 13 residues within 4Å: Chain C: F.208, D.210, D.214, T.218, F.235, E.236, Q.242, D.243, K.251, C.252, H.253, Y.276, D.277 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.235, C:F.235, C:K.251 Hydrogen bonds: C:D.214, C:E.236, C:Q.242, C:K.251, C:C.252, C:H.253, C:D.277 Salt bridges: C:D.243 pi-Cation interactions: C:Y.276

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

NAG-NDG.2: 3 residues within 4Å: Chain B: M.228, E.230, N.231 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 4 residues within 4Å: Chain B: D.128, G.130, D.265 Chain C: E.45 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.128, B:G.130, B:D.265, C:E.45 CA.5: 4 residues within 4Å: Chain C: D.231, D.233, F.235, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

 - 

Release Date

2007-07-17

Peptides

Fibrin alpha chain: A
Fibrin beta chain: B
Fibrin, gamma polypeptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Fibrin alpha chain

Fibrin beta chain

Fibrin, gamma polypeptide

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