SMTL ID : 3qvb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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.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.2: 13 residues within 4Å: Chain A: L.10, T.11, T.12, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.83 Hydrogen bonds: A:L.10, A:L.10, A:T.12, A:T.12, A:Y.16, A:A.104, A:D.105, A:G.216 Salt bridges: A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.9: 13 residues within 4Å: Chain B: L.10, T.11, T.12, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.83 Hydrogen bonds: B:L.10, B:L.10, B:T.12, B:T.12, B:Y.16, B:A.104, B:D.105, B:G.216 Salt bridges: B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

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

EDO.3: 3 residues within 4Å: Chain A: H.30, A.110, N.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.30, A:N.111 EDO.4: 4 residues within 4Å: Chain A: T.94, S.143, V.144, E.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.144, A:E.145 EDO.5: 5 residues within 4Å: Chain A: E.120, L.121, S.174, W.175, K.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.121, A:K.182 Water bridges: A:E.120 EDO.6: 4 residues within 4Å: Chain A: I.60, H.89, S.92, L.93 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.70, A:S.92, A:Q.95, A:Q.95 EDO.7: 3 residues within 4Å: Chain A: S.45, D.46, S.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.46, A:S.47, A:S.47 EDO.10: 3 residues within 4Å: Chain B: H.30, A.110, N.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.30, B:N.111 EDO.11: 4 residues within 4Å: Chain B: T.94, S.143, V.144, E.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.144, B:E.145 EDO.12: 5 residues within 4Å: Chain B: E.120, L.121, S.174, W.175, K.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.121, B:K.182 Water bridges: B:E.120 EDO.13: 4 residues within 4Å: Chain B: I.60, H.89, S.92, L.93 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.70, B:S.92, B:Q.95, B:Q.95 EDO.14: 3 residues within 4Å: Chain B: S.45, D.46, S.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.46, B:S.47, B:S.47

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

2011-03-23

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogenin-1

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