SMTL ID : 3rmv.1

Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 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.6: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UDP.7 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: 14 residues within 4Å: Chain A: L.10, T.11, T.12, N.13, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:L.10, A:T.12, A:T.12, A:N.13, A:Y.16, A:A.104, A:D.105, A:G.216 Water bridges: A:N.134, A:G.216 Salt bridges: A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.7: 14 residues within 4Å: Chain B: L.10, T.11, T.12, N.13, Y.16, V.83, D.103, A.104, D.105, H.213, L.215, G.216, K.219 Ligands: MN.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:N.13, B:Y.16, B:A.104, B:D.105, B:G.216 Water bridges: B:N.134, B:G.216 Salt bridges: B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

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

EDO.3: 6 residues within 4Å: Chain A: E.120, L.121, F.172, S.174, W.175, K.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.120, A:L.121, A:K.182 EDO.4: 5 residues within 4Å: Chain A: D.179, I.180 Chain B: D.179, I.180 Ligands: EDO.9 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.179, A:I.180, B:D.179, B:I.180 Water bridges: A:D.179, B:D.179 EDO.8: 6 residues within 4Å: Chain B: E.120, L.121, F.172, S.174, W.175, K.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.120, B:L.121, B:K.182 EDO.9: 5 residues within 4Å: Chain A: D.179, I.180 Chain B: D.179, I.180 Ligands: EDO.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.179, A:I.180, B:D.179, B:I.180 Water bridges: A:D.179, B:D.179

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: H.152, E.156 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.152, A:E.156, H2O.8, H2O.8 MG.10: 2 residues within 4Å: Chain B: H.152, E.156 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.152, B:E.156, H2O.17, H2O.17

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

2011-05-18

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogenin-1

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