SMTL ID : 3t7o.1

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP-Glucose and glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

GLC.1: 9 residues within 4Å: Chain A: M.76, R.78, D.126, P.127, N.134, Q.165 Chain B: S.197, Y.198 Ligands: UPG.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.78, A:D.126, A:N.134, A:Q.165 Water bridges: B:S.197, B:S.197

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

MN.2: 4 residues within 4Å: Chain A: D.103, D.105, H.213 Ligands: UPG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.105, A:D.105, A:H.213 MN.14: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UPG.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.103, B:D.105, B:D.105, B:H.213

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

UPG.3: 26 residues within 4Å: Chain A: 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, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, H.213, L.215, G.216, K.219 Ligands: GLC.1, MN.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.81 Hydrogen bonds: A:L.10, A:T.12, A:T.12, A:N.13, A:Y.16, A:K.87, A:K.87, A:A.104, A:D.105, A:D.105, A:N.134, A:N.134, A:S.135, A:D.161, A:Q.165, A:G.216 Salt bridges: A:R.78, A:R.78, A:R.78, A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UPG.15: 25 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, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, H.213, L.215, G.216, K.219 Ligands: MN.14 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.81 Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:T.12, B:N.13, B:Y.16, B:Y.16, B:K.87, B:K.87, B:A.104, B:D.105, B:D.105, B:N.134, B:N.134, B:S.135, B:D.161, B:Q.165, B:G.216 Water bridges: B:D.126, B:Q.165 Salt bridges: B:R.78, B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

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

EDO.4: 4 residues within 4Å: Chain A: T.94, S.143, V.144, E.145 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: D.179, I.180 Chain B: I.180 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: R.35 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: E.120, L.121, F.172, S.174, W.175, K.182 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: H.30, A.110, N.111 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: R.34 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: Q.5, K.98, F.116 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: F.171, F.172, S.173, S.174 Ligands: EDO.7 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Q.29, H.30, L.109 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: P.42, R.49 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: H.30, R.31, A.110, N.111 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: E.120, L.121, S.174, W.175, K.182 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: S.92, T.94, Q.95 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: R.35, E.58, Y.96 Ligands: EDO.20, EDO.24 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: R.35 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: D.4, T.94, Q.95, S.97 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: E.53, V.59, M.61 Ligand excluded by PLIP EDO.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: E.58, Q.95 Ligands: EDO.19 Ligand excluded by PLIP

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

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