SMTL ID : 7e9l.1

Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short peptide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: E.246, N.296, A.297, S.298, P.315, P.430 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: E.21, N.58 Chain B: Q.225, H.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.228, B:H.228 NAG.3: 3 residues within 4Å: Chain A: L.500, Q.501, N.502 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.501, A:Q.501 NAG.6: 4 residues within 4Å: Chain A: Q.225, H.228 Chain B: E.21, N.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.228 NAG.7: 4 residues within 4Å: Chain B: E.245, E.246, N.296, S.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.245, B:E.246, B:N.296 NAG.8: 3 residues within 4Å: Chain B: L.500, Q.501, N.502 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.501, B:Q.501, B:N.502

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

UDP.4: 16 residues within 4Å: Chain A: D.121, N.122, L.123, R.253, T.254, Q.255, N.256, R.257, L.282, E.283, G.305, A.306, Q.307, Y.406 Ligands: TRS.5, MAN.10 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.122, 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 Water bridges: A:R.253, A:R.253, A:R.253, A:R.253, A:L.282 Salt bridges: A:R.253, A:R.253, A:R.257, A:R.257 UDP.9: 14 residues within 4Å: Chain B: D.121, N.122, L.123, R.253, T.254, Q.255, N.256, R.257, L.282, E.283, G.305, A.306, Q.307, Y.406 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.122, B:L.123, B:T.254, B:Q.255, B:N.256, B:E.283, B:E.283, B:A.306, B:Q.307, B:Q.307, B:Y.406 Water bridges: B:R.253, B:R.253 Salt bridges: B:R.253, B:R.253, B:R.257, B:R.257

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

TRS.5: 9 residues within 4Å: Chain A: M.124, H.304, G.305, A.306, P.335, Y.336, W.401 Ligands: UDP.4, MAN.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.305, A:Y.336 Water bridges: A:Q.210, A:W.401

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.10: 10 residues within 4Å: Chain A: N.122, H.125, Y.204, Q.210, C.395, C.396 Chain C: X.1, T.3 Ligands: UDP.4, TRS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.122, A:Q.210

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
mono-mannosyl peptide (379Man short peptide): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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

mono-mannosyl peptide (379Man short peptide)

Related Entries With Identical Sequence