SMTL ID : 3u2x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.103, D.105, H.213 Ligands: UDP.2, ASO.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.105, A:D.105, A:H.213 MN.12: 5 residues within 4Å: Chain B: D.103, D.105, H.213 Ligands: UDP.13, ASO.14 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: 18 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, ASO.3 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:N.13, A:Y.16, A:A.104, A:D.105, A:D.105, A:G.216 Water bridges: A:R.78, 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.13: 18 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.12, ASO.14 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.81 Hydrogen bonds: B:L.10, B:T.12, B:T.12, B:T.12, B:N.13, B:Y.16, B:A.104, B:D.105, B:G.216 Water bridges: B:R.78 Salt bridges: B:R.78, B:R.78, B:H.213, B:K.219, B:K.219 pi-Stacking: B:Y.16

2 x ASO: 1,5-anhydro-D-glucitol(Non-covalent)

ASO.3: 14 residues within 4Å: Chain A: T.84, K.87, D.103, N.134, S.135, G.136, D.161, G.163, D.164, Q.165, H.213 Ligands: MN.1, UDP.2, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.87, A:D.103, A:N.134, A:N.134, A:D.161, A:D.164, A:Q.165 ASO.14: 14 residues within 4Å: Chain B: M.76, T.84, K.87, D.103, N.134, S.135, D.161, G.163, D.164, Q.165, H.213 Ligands: MN.12, UDP.13, EDO.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.84, B:K.87, B:D.103, B:N.134, B:N.134, B:G.136, B:D.161, B:D.164, B:Q.165

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

EDO.4: 8 residues within 4Å: Chain A: D.126, G.128, N.134, Q.165, L.215 Chain B: S.197, Y.198 Ligands: ASO.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.197, A:G.128, A:N.134, A:Q.165, A:Q.165 EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: Q.29, N.252, I.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.29, A:Q.29, A:N.252 Water bridges: A:N.252, A:T.256 EDO.7: 1 residues within 4Å: Chain A: T.54 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: I.60, S.92, L.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.92 EDO.9: 6 residues within 4Å: Chain A: E.120, L.121, S.174, W.175, K.182 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.121, A:K.182, A:K.182 Water bridges: A:T.178 EDO.10: 5 residues within 4Å: Chain A: F.171, F.172, S.173, S.174 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.174, A:S.174 EDO.11: 3 residues within 4Å: Chain A: L.151, H.152, S.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.152, A:S.155 EDO.15: 7 residues within 4Å: Chain A: S.197, Y.198 Chain B: D.126, G.128, N.134, Q.165 Ligands: ASO.14 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.128, B:N.134, B:Q.165, B:Q.165, A:S.197 EDO.16: 3 residues within 4Å: Chain B: P.42, R.49, M.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.49, B:R.49 EDO.17: 6 residues within 4Å: Chain A: A.176, T.177 Chain B: R.118, I.180, H.183, P.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.118, B:R.118, B:I.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and 1'-deoxyglucose. To be Published

Release Date

2011-11-02

Peptides

Glycogenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogenin-1

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