SMTL ID : 3v8z.2 (1 other biounit)

Structure of apo-glycogenin truncated at residue 270 complexed with UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: H.49, A.129, N.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.130 GOL.2: 5 residues within 4Å: Chain A: D.150, N.188, T.189, N.192 Chain B: F.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:A.195 GOL.6: 3 residues within 4Å: Chain B: H.49, A.129, N.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.130 GOL.7: 5 residues within 4Å: Chain A: F.224 Chain B: D.150, N.188, T.189, N.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.188 Water bridges: B:A.195 GOL.11: 3 residues within 4Å: Chain C: H.49, A.129, N.130 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.49, C:N.130 GOL.12: 5 residues within 4Å: Chain C: D.150, N.188, T.189, N.192 Chain D: F.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.188 Water bridges: C:A.195 GOL.16: 3 residues within 4Å: Chain D: H.49, A.129, N.130 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.49, D:N.130 GOL.17: 5 residues within 4Å: Chain C: F.224 Chain D: D.150, N.188, T.189, N.192 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.188 Water bridges: D:A.195

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: D.198, I.199 Ligands: CL.8, CL.13, CL.18 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: D.198, I.199 Ligands: CL.3, CL.13, CL.18 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: D.198, I.199 Ligands: CL.3, CL.8, CL.18 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: D.198, I.199 Ligands: CL.3, CL.8, CL.13 Ligand excluded by PLIP

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

MN.4: 4 residues within 4Å: Chain A: D.122, D.124, H.232 Ligands: UDP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.122, A:D.124, A:D.124, A:H.232 MN.9: 4 residues within 4Å: Chain B: D.122, D.124, H.232 Ligands: UDP.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.122, B:D.124, B:D.124, B:H.232 MN.14: 4 residues within 4Å: Chain C: D.122, D.124, H.232 Ligands: UDP.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.122, C:D.124, C:D.124, C:H.232 MN.19: 4 residues within 4Å: Chain D: D.122, D.124, H.232 Ligands: UDP.20 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.122, D:D.124, D:D.124, D:H.232

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.5: 14 residues within 4Å: Chain A: L.29, T.30, T.31, N.32, Y.35, V.102, D.122, A.123, D.124, H.232, L.234, G.235, K.238 Ligands: MN.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.102 Hydrogen bonds: A:L.29, A:T.31, A:T.31, A:T.31, A:N.32, A:Y.35, A:A.123, A:D.124, A:G.235 Salt bridges: A:H.232, A:K.238, A:K.238 pi-Stacking: A:Y.35 UDP.10: 14 residues within 4Å: Chain B: L.29, T.30, T.31, N.32, Y.35, V.102, D.122, A.123, D.124, H.232, L.234, G.235, K.238 Ligands: MN.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.102 Hydrogen bonds: B:L.29, B:T.31, B:T.31, B:T.31, B:N.32, B:Y.35, B:A.123, B:D.124, B:G.235 Salt bridges: B:H.232, B:K.238, B:K.238 pi-Stacking: B:Y.35 UDP.15: 14 residues within 4Å: Chain C: L.29, T.30, T.31, N.32, Y.35, V.102, D.122, A.123, D.124, H.232, L.234, G.235, K.238 Ligands: MN.14 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.102 Hydrogen bonds: C:L.29, C:T.31, C:T.31, C:N.32, C:A.123, C:D.124, C:G.235 Salt bridges: C:H.232, C:K.238, C:K.238 pi-Stacking: C:Y.35 UDP.20: 14 residues within 4Å: Chain D: L.29, T.30, T.31, N.32, Y.35, V.102, D.122, A.123, D.124, H.232, L.234, G.235, K.238 Ligands: MN.19 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.102 Hydrogen bonds: D:L.29, D:T.31, D:T.31, D:N.32, D:A.123, D:D.124, D:G.235 Salt bridges: D:H.232, D:K.238, D:K.238 pi-Stacking: D:Y.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrizo, M.E. et al., Structural and biochemical insight into glycogenin inactivation by the glycogenosis-causing T82M mutation. Febs Lett. (2012)

Release Date

2012-01-25

Peptides

Glycogenin-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glycogenin-1

Related Entries With Identical Sequence