SMTL ID : 3t7n.1

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a monoclinic closed form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

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

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

UDP.2: 18 residues within 4Å: Chain A: L.10, T.11, T.12, N.13, Y.16, R.78, E.80, L.81, V.83, T.84, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:L.10, A:L.10, A:T.12, A:T.12, A:T.12, A:N.13, A:Y.16, A:Y.16, A:A.104, A:D.105, A:D.105, A:G.216 Water bridges: A:R.78 Salt bridges: A:R.78, A:R.78, A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.4: 18 residues within 4Å: Chain B: L.10, T.11, T.12, N.13, Y.16, R.78, L.81, V.83, T.84, K.87, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.3 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.83 Hydrogen bonds: B:L.10, B:L.10, B:T.12, B:T.12, B:N.13, B:A.104, B:D.105, B:D.105, B:G.216 Water bridges: B:T.12, B:Q.165 Salt bridges: B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-08-31

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogenin-1

Related Entries With Identical Sequence