SMTL ID : 6rq7.1

Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin - resurrection of highly anisotropic data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: Q.85, N.88 No protein-ligand interaction detected (PLIP)

3 x GD: GADOLINIUM ATOM(Non-functional Binders)

GD.2: 1 residues within 4Å: Ligands: DO3.7 No protein-ligand interaction detected (PLIP) GD.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GD.4: 1 residues within 4Å: Ligands: DO3.8 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: Y.106, L.207, K.208, N.467 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.106 NAG.6: 2 residues within 4Å: Chain A: N.381, E.385 No protein-ligand interaction detected (PLIP)

3 x DO3: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID(Non-covalent)

DO3.7: 4 residues within 4Å: Chain A: N.295, N.297 Ligands: GD.2, DO3.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.295, A:N.297 DO3.8: 7 residues within 4Å: Chain A: Y.198, I.221, I.294, I.346, N.452 Ligands: GD.4, DO3.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.452 Salt bridges: A:K.225 DO3.9: 4 residues within 4Å: Chain A: D.358, T.480, N.481, F.484 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.358, A:D.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naschberger, A. et al., Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-07-10

Peptides

Afamin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Afamin

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