SMTL ID : 7e9j.1

Crystal Structure of POMGNT2 in complex with UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: E.21, N.58 Chain B: Q.225, H.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.228 NAG.2: 3 residues within 4Å: Chain A: L.500, Q.501, N.502 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.501, A:Q.501 Water bridges: A:N.502 NAG.5: 4 residues within 4Å: Chain A: Q.225, H.228 Chain B: E.21, N.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.58 NAG.6: 3 residues within 4Å: Chain B: L.500, Q.501, N.502 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.501, B:Q.501

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 15 residues within 4Å: Chain A: D.121, N.122, L.123, H.161, R.253, T.254, Q.255, N.256, R.257, L.282, E.283, G.305, A.306, Q.307, Y.406 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.122, A:L.123, A:T.254, A:Q.255, A:N.256, A:E.283, A:A.306, A:Q.307, A:Q.307, A:Y.406, A:Y.406 Water bridges: A:R.253, A:R.253, A:L.282, A:Y.406 Salt bridges: A:R.253, A:R.253, A:R.257, A:R.257 UDP.7: 15 residues within 4Å: Chain B: D.121, N.122, L.123, H.161, R.253, T.254, Q.255, N.256, R.257, L.282, E.283, G.305, A.306, Q.307, Y.406 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:N.122, B:L.123, B:R.253, B:T.254, B:Q.255, B:N.256, B:R.257, B:E.283, B:A.306, B:Q.307, B:Q.307 Water bridges: B:N.256, B:N.256 Salt bridges: B:R.253, B:R.253, B:R.257

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 1 residues within 4Å: Chain A: E.507 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.507 Water bridges: A:E.507

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imae, R. et al., The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan. Genes Cells (2021)

Release Date

2021-05-05

Peptides

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2

Related Entries With Identical Sequence