SMTL ID : 2rl8.1

Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to M6P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: R.79, N.81, E.82 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.82 Hydrogen bonds: A:N.81, A:E.82, A:E.82 NAG.4: 3 residues within 4Å: Chain B: R.79, N.81, E.82 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.82 Hydrogen bonds: B:E.82, B:E.82

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: D.103 Ligands: M6D.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.103, H2O.2, H2O.3, H2O.4 MN.5: 2 residues within 4Å: Chain B: D.103 Ligands: M6D.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.103, H2O.9, H2O.9

2 x M6D: 6-O-phosphono-beta-D-mannopyranose(Non-covalent)

M6D.3: 12 residues within 4Å: Chain A: Y.45, Q.66, K.73, Y.102, D.103, N.104, H.105, R.111, E.133, R.135, Y.143 Ligands: MN.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Y.45, A:Q.66, A:Q.66, A:D.103, A:N.104, A:N.104, A:H.105, A:R.111, A:E.133, A:R.135, A:Y.143 Water bridges: A:K.73, A:T.75, A:T.75 Salt bridges: A:K.73, A:H.105, A:R.111 M6D.6: 11 residues within 4Å: Chain B: Y.45, Q.66, Y.102, D.103, N.104, H.105, R.111, E.133, R.135, Y.143 Ligands: MN.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.66, B:Q.66, B:D.103, B:N.104, B:N.104, B:H.105, B:R.111, B:E.133, B:R.135, B:Y.143 Water bridges: B:T.75, B:T.75, B:T.75 Salt bridges: B:H.105, B:R.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olson, L.J. et al., Structural Insights into the Mechanism of pH-dependent Ligand Binding and Release by the Cation-dependent Mannose 6-Phosphate Receptor. J.Biol.Chem. (2008)

Release Date

2008-02-12

Peptides

Cation-dependent mannose-6-phosphate receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cation-dependent mannose-6-phosphate receptor

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