SMTL ID : 3u2v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC-GLC-GLC-GLC-GLC.1: 29 residues within 4Å: Chain A: Y.196, S.197, Y.198, H.237 Chain B: M.76, K.77, R.78, L.81, T.84, K.87, D.103, D.126, G.128, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, I.193, H.213, L.215, G.216, R.217, V.218, H.237, P.239 Ligands: UDP.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.84, B:K.87, B:K.87, B:D.103, B:N.134, B:N.134, B:D.161, B:Q.165 GLC-GLC-GLC-GLC-GLC-GLC.2: 27 residues within 4Å: Chain A: M.76, R.78, L.81, T.84, K.87, D.103, D.126, G.128, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, I.193, H.213, L.215, G.216, R.217, H.237, P.239 Chain B: Y.196, S.197, Y.198, H.237 Ligands: UDP.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.87, A:K.87, A:D.103, A:N.134, A:D.161, A:Q.165, A:Q.165

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

MN.3: 4 residues within 4Å: Chain A: D.103, D.105, H.213 Ligands: UDP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.105, A:D.105, A:H.213 MN.8: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UDP.9 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.4: 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: GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2, MN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.81, A:V.83 Hydrogen bonds: A:L.10, A:T.12, A:T.12, A:N.13, A:A.104, A:D.105, A:G.216 Water bridges: A:T.12 Salt bridges: A:R.78, A:R.78, A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.9: 19 residues within 4Å: Chain B: 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: GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC.1, MN.8 17 PLIP interactions: 17 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:A.104, B:D.105, B:D.105, B:G.216 Salt bridges: B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Y.225, W.251, F.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.225 Water bridges: A:Y.225, A:Y.225 GOL.6: 4 residues within 4Å: Chain A: H.30, R.31, A.110, N.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.30, A:R.31, A:R.31, A:N.111 GOL.10: 2 residues within 4Å: Chain B: P.42, R.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.49, B:R.49 GOL.11: 3 residues within 4Å: Chain B: R.31, T.32, T.33 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.33, B:R.34, B:D.57 GOL.12: 5 residues within 4Å: Chain B: I.60, V.62, S.92, L.93, Q.95 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.92, B:S.92, B:Q.95 Water bridges: B:T.94, B:T.94 GOL.13: 10 residues within 4Å: Chain A: P.125, P.130, D.131, W.175, H.183 Chain B: P.125, P.130, D.131, W.175, H.183 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.131, B:D.131, B:H.183, A:P.130, A:H.183 GOL.14: 4 residues within 4Å: Chain B: T.94, S.143, V.144, E.145 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.143, B:V.144, B:E.145 Water bridges: B:T.94, B:T.94 GOL.15: 3 residues within 4Å: Chain B: L.153, T.170, F.171 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.170, B:S.173

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: D.179, I.180 Chain B: D.179, I.180 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.179, A:I.180, B:D.179, B:I.180 SO4.16: 4 residues within 4Å: Chain B: H.30, R.31, A.110, N.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.111 Water bridges: B:R.31, B:R.31 Salt bridges: B:H.30, B:R.31

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

2011-12-07

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogenin-1

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