SMTL ID : 5ggi.2 (1 other biounit)

Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-2-mer

Ligands

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

UDP.1: 18 residues within 4Å: Chain A: I.216, A.217, G.218, R.220, D.247, R.276, V.277, H.280, E.302, E.303, D.304, H.409, G.414, L.415, N.416, M.417 Ligands: MN.2, MAN.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.277 Hydrogen bonds: A:I.216, A:A.217, A:R.220, A:D.247, A:E.303, A:E.303, A:H.409, A:L.415, A:N.416, A:N.416 Salt bridges: A:R.220

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

MN.2: 3 residues within 4Å: Chain A: D.304, H.409 Ligands: UDP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.304, A:H.409

2 x MAN: alpha-D-mannopyranose(Post Translational Modification)(Non-covalent)

MAN.3: 9 residues within 4Å: Chain A: R.38, Y.61, D.88, R.116, W.143 Chain B: P.4, T.5, P.6, V.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.38, A:R.116, A:W.143 MAN.4: 10 residues within 4Å: Chain A: D.385, M.386, R.389, N.416, M.417, F.421, W.509, R.514 Chain C: T.5 Ligands: UDP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.385, A:D.385, A:R.389, A:N.416, A:R.514, A:R.514

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuwabara, N. et al., Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-10

Peptides

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1: A
mannosyl-peptide: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

C
G

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

mannosyl-peptide

Related Entries With Identical Sequence