SMTL ID : 2rl9.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MAN- MAN- M6P: 6-O-phosphono-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose

MAN-MAN-M6P.1: 13 residues within 4Å: Chain A: M.44, Y.45, Q.66, Q.68, Y.102, D.103, N.104, H.105, R.111, E.133, R.135, Y.143 Ligands: MN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.66, A:Q.66, A:D.103, A:N.104, A:N.104, A:R.111, A:E.133, A:R.135, A:Y.143, A:Y.45, A:Y.45, A:Q.68, A:Q.68, A:R.135 Water bridges: A:Y.45, A:H.105, A:H.105, A:R.135 Salt bridges: A:H.105 MAN-MAN-M6P.2: 13 residues within 4Å: Chain B: P.42, Y.45, Q.66, Q.68, Y.102, D.103, N.104, H.105, R.111, E.133, R.135, Y.143 Ligands: MN.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.66, B:Q.66, B:D.103, B:N.104, B:N.104, B:R.111, B:E.133, B:Y.143, B:P.42, B:Q.68, B:R.135 Salt bridges: B:H.105

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

NAG.3: 3 residues within 4Å: Chain A: R.79, N.81, E.82 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.82 Hydrogen bonds: A:E.82, A:E.82 NAG.5: 3 residues within 4Å: Chain B: R.79, N.81, E.82 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.82 Hydrogen bonds: B:N.81, B:E.82, B:E.82

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

MN.4: 3 residues within 4Å: Chain A: D.103 Ligands: MAN-MAN-M6P.1, MAN-MAN-M6P.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.103 MN.6: 2 residues within 4Å: Chain B: D.103 Ligands: MAN-MAN-M6P.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.103

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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