SMTL ID : 5gz9.1

Crystal structure of catalytic domain of Protein O-mannosyl Kinase in complexes with AMP-PNP, Magnesium ions and glycopeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 23 residues within 4Å: Chain A: V.42, G.43, G.45, A.46, V.47, K.48, V.50, A.61, T.104, E.105, Y.106, H.107, S.111, D.159, K.165, S.168, Q.169, L.171, N.181, D.182, D.184 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.46, A:V.47, A:K.48, A:K.48, A:E.105, A:H.107, A:D.159, A:K.165, A:K.165, A:S.168, A:S.168, A:N.181 Water bridges: A:G.45, A:G.45, A:T.104 Salt bridges: A:K.48

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.182, D.184 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.182, A:D.182, A:D.184 MG.3: 4 residues within 4Å: Chain A: S.168, Q.169, D.182 Ligands: ANP.1 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.4: 7 residues within 4Å: Chain A: C.158, D.159, N.161, A.185, C.199, G.200, R.202 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.161, A:N.161, A:C.199 Water bridges: A:S.160, A:N.161, A:K.198, A:C.199 Salt bridges: A:R.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, M. et al., 3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy. Genes Cells (2017)

Release Date

2017-03-29

Peptides

Protein O-mannose kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein O-mannose kinase

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