SMTL ID : 3t7m.1

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a triclinic closed form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.15: 4 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UDP.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 UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 17 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: MN.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.81 Hydrogen bonds: A:L.10, A:T.12, A:T.12, A:T.12, A:N.13, A:Y.16, A:Y.16, A:A.104, A:D.105, A:G.216 Water bridges: A:R.78 Salt bridges: A:R.78, A:R.78, A:H.213, A:K.219, A:K.219 pi-Stacking: A:Y.16 UDP.16: 17 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: MN.15 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.81 Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:N.13, B:A.104, B:D.105, B:G.216 Water bridges: B:K.87 Salt bridges: B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

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

EDO.3: 4 residues within 4Å: Chain A: T.94, S.143, V.144, E.145 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: I.180 Chain B: T.178, D.179, I.180 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: E.120, L.121, S.174, W.175, T.178, K.182 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: N.257 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: L.153 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: P.79, E.80 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: H.30, R.31, A.110, N.111 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.114, L.115, R.118, P.185, Y.188 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: D.131, C.132, A.176 Chain B: F.205 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: G.216, R.217 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.192, F.214, Y.223, N.240 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: D.126, G.128, N.134, Q.165, L.215 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: E.120, L.121, S.174, W.175, T.178, K.182 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: P.42, R.49 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: T.94, S.143, V.144, E.145 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: F.205 Chain B: D.131, C.132, A.176 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: D.114, L.115, R.118, P.185, Y.188 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: T.94, Q.95, Y.96, S.97 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: H.30, A.110, N.111 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: R.78, I.193, G.216, R.217 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: P.42, Q.43, V.44, S.45, D.46, R.49 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: S.1, R.34 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: S.197, Y.198 Chain B: D.126, G.128, N.134, Q.165 Ligand excluded by PLIP

Links

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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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