SMTL ID : 5e4k.1

Structure of ligand binding region of uPARAP at pH 7.4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.418, Q.422, N.445, E.451, D.452 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.418, A:D.418, A:E.451, A:D.452, H2O.1 CA.2: 5 residues within 4Å: Chain A: E.442, N.444, E.451, N.464, D.465 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.442, A:E.451, A:D.465, A:D.465, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: Q.298, D.300, E.305, N.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.298, A:Q.319

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

NAG.4: 2 residues within 4Å: Chain A: N.41, L.44 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.469 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 2 residues within 4Å: Chain A: E.313, S.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.315

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.7: 6 residues within 4Å: Chain A: Q.151, Y.165, G.177, R.178, Y.191, T.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, C. et al., Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding. Biochem.J. (2016)

Release Date

2016-08-10

Peptides

C-type mannose receptor 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C-type mannose receptor 2

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