SMTL ID : 5vcs.1

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with Bound Acceptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN-NAG-MAN.1: 15 residues within 4Å: Chain A: R.170, D.189, F.191, H.193, E.196, F.199, T.287, N.290, Y.316, N.317, D.319, W.320, R.398, N.400, G.402 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.316, A:Y.316, A:N.317, A:N.290, A:D.319, A:D.319, A:R.170, A:D.189, A:D.189, A:H.193, A:E.196, A:N.400, A:G.402 Water bridges: A:T.287 Hydrophobic interactions: A:F.191 NAG-BMA-MAN-NAG-MAN.2: 15 residues within 4Å: Chain B: R.170, D.189, F.191, H.193, E.196, F.199, T.287, N.290, Y.316, N.317, D.319, W.320, R.398, N.400, G.402 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.316, B:N.317, B:N.290, B:D.319, B:R.170, B:D.189, B:H.193, B:E.196, B:N.400, B:G.402 Hydrophobic interactions: B:F.191

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

NAG.3: 4 residues within 4Å: Chain A: N.58, T.60, L.61, R.64 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain B: N.58, T.60, L.61, R.64, N.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.58, B:R.64, B:R.64, B:N.158

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: A.113, Q.114, G.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.115 Salt bridges: A:D.117 DMS.5: 4 residues within 4Å: Chain A: W.128, S.129, T.130, E.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.130, A:T.130 DMS.6: 7 residues within 4Å: Chain A: E.55, A.56, D.57, N.58, L.61, R.62 Chain B: S.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.58, A:R.62 Salt bridges: A:D.57

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain B: A.113, Q.114, G.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-11

Peptides

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase

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