SMTL ID : 6eql.1

Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant complexed with manganese and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 14 residues within 4Å: Chain A: L.10, T.11, T.12, N.13, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:L.10, A:T.12, A:T.12, A:T.12, A:N.13, A:Y.16, A:A.104, A:D.105, A:G.216, A:G.216 Salt bridges: A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.3: 16 residues within 4Å: Chain B: L.10, T.11, T.12, N.13, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.4, 2PE.5, EDO.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.83 Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:T.12, B:N.13, B:Y.16, B:A.104, B:D.105, B:G.216 Salt bridges: B:K.219, B:K.219 pi-Stacking: B:Y.16

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

MN.2: 4 residues within 4Å: Chain A: D.103, D.105, H.213 Ligands: UDP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.105, A:D.105, A:H.213 MN.4: 5 residues within 4Å: Chain B: D.103, D.105, H.213, L.215 Ligands: UDP.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.103, B:D.105, B:D.105, B:H.213

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.5: 10 residues within 4Å: Chain B: D.126, N.134, S.135, G.163, D.164, Q.165, G.216, R.217 Ligands: UDP.3, EDO.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.135, B:D.164, B:Q.165 Water bridges: B:N.134

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 2 residues within 4Å: Ligands: UDP.3, 2PE.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bilyard, M.K. et al., Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis. Nature (2018)

Release Date

2017-12-20

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogenin-1

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