SMTL ID : 3u2w.1

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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.7: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UDP.8 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: 19 residues within 4Å: Chain A: L.10, T.11, T.12, N.13, Y.16, R.78, L.81, V.83, T.84, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.1, GLC.5, LCN.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.81 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 Water bridges: A:R.78, 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.8: 19 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.7, GLC.10 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.83 Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:N.13, B:Y.16, B:A.104, B:D.105, B:D.105, B:G.216 Water bridges: B:T.12, B:R.78, B:R.78 Salt bridges: B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: D.126, G.128, N.134, Q.165, L.215 Chain B: S.197, Y.198 Ligands: GOL.4, GLC.5, LCN.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.128, A:N.134, A:Q.165, A:Q.165 GOL.4: 7 residues within 4Å: Chain A: M.76, R.78, I.195, G.216, R.217 Chain B: S.197 Ligands: GOL.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.78, B:S.197 Water bridges: A:K.77 GOL.9: 6 residues within 4Å: Chain B: S.45, S.47, M.48, V.51, L.261, L.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:S.45, B:L.262 Water bridges: B:V.51

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.5: 17 residues within 4Å: Chain A: M.76, T.84, K.87, D.103, D.126, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, H.213, L.215 Ligands: UDP.2, GOL.3, LCN.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.87, A:K.87, A:D.103, A:N.134, A:Q.165, A:Q.165 GLC.10: 13 residues within 4Å: Chain B: T.84, K.87, D.103, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, H.213, L.215 Ligands: UDP.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.87, B:K.87, B:N.134, B:D.161, B:Q.165, B:Q.165, B:Q.165, B:Q.165 Water bridges: B:R.78

1 x LCN: 1,5-anhydro-D-arabino-hex-1-enitol(Non-covalent)

LCN.6: 16 residues within 4Å: Chain A: M.76, L.81, T.84, K.87, D.103, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, L.215 Ligands: UDP.2, GOL.3, GLC.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.84, A:K.87, A:K.87, A:N.134, A:S.135, A:D.161, A:Q.165, A:Q.165

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

2011-11-02

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogenin-1

Related Entries With Identical Sequence