SMTL ID : 6zqp.1

Structure of the Pmt2-MIR domain with bound ligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 3 residues within 4Å: Chain A: S.80, N.130, V.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130 Water bridges: A:S.80, A:S.80

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.43, H.45, D.65, N.67, F.185, Q.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.45, A:D.65, A:N.67, A:Q.187 GOL.3: 3 residues within 4Å: Chain A: F.197, K.198, R.199 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.198, A:R.199, A:R.199, A:R.199 Water bridges: A:P.196 GOL.4: 4 residues within 4Å: Chain A: V.117, S.118, K.119, T.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.117, A:K.119, A:T.120

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.21, T.157, H.210 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.21, A:R.21, A:T.157 Water bridges: A:D.22, A:T.157, A:T.157 Salt bridges: A:R.21, A:H.210 SO4.6: 1 residues within 4Å: Chain A: R.186 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.186 SO4.7: 5 residues within 4Å: Chain A: Q.55, H.109, H.111, D.134, K.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.55 Water bridges: A:K.136 Salt bridges: A:H.109, A:H.111 SO4.8: 4 residues within 4Å: Chain A: D.51, G.52, A.114, K.119 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.52 Water bridges: A:A.114, A:A.114, A:A.115, A:K.119, A:K.119 Salt bridges: A:K.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiapparino, A. et al., Functional implications of MIR domains in protein O -mannosylation. Elife (2020)

Release Date

2020-12-23

Peptides

PMT2 isoform 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PMT2 isoform 1