SMTL ID : 3rmw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

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

UPG.1: 22 residues within 4Å: Chain A: L.10, T.11, T.12, N.13, Y.16, V.83, 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.2, EDO.8 23 PLIP interactions: 23 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:N.134, A:G.163, A:Q.165, A:G.216, A:G.216 Water bridges: A:T.12, A:D.103, A:D.126, A:D.164, A:G.166, A:K.219, A:K.219 Salt bridges: A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UPG.16: 22 residues within 4Å: Chain B: L.10, T.11, T.12, N.13, Y.16, V.83, 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.17, EDO.23 23 PLIP interactions: 23 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:N.134, B:G.163, B:Q.165, B:G.216, B:G.216 Water bridges: B:T.12, B:D.103, B:D.126, B:D.164, B:G.166, B:K.219, B:K.219 Salt bridges: B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

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

MN.2: 4 residues within 4Å: Chain A: D.103, D.105, H.213 Ligands: UPG.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.105, A:D.105, A:H.213 MN.17: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UPG.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.103, B:D.105, B:D.105, B:H.213

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.6, H2O.6 MG.18: 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.13, H2O.13

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

EDO.4: 4 residues within 4Å: Chain A: I.60, V.62, H.89, L.93 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: T.94, P.142, S.143, V.144 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: P.125, P.130, D.131, W.175, H.183 Chain B: P.125, P.130, H.183 Ligands: EDO.21 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: E.120, L.121, F.172, S.174, W.175, K.182 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: V.83, M.84, K.87, G.162, G.163, D.164 Ligands: UPG.1 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: Q.149, H.152 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: F.171, F.172 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: D.57, E.58, V.59 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: P.42, D.63, L.65 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: D.46, K.50, E.53 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: L.65, D.66, S.67 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: E.145 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: I.60, V.62, H.89, L.93 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: T.94, P.142, S.143, V.144 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: P.125, P.130, H.183 Chain B: P.125, P.130, D.131, W.175, H.183 Ligands: EDO.6 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: E.120, L.121, F.172, S.174, W.175, K.182 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: V.83, M.84, K.87, G.162, G.163, D.164 Ligands: UPG.16 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: Q.149, H.152 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: F.171, F.172 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: D.57, E.58, V.59 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: P.42, D.63, L.65 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: D.46, K.50, E.53 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: L.65, D.66, S.67 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain B: E.145 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

2011-05-11

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogenin-1

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