SMTL ID : 1y6g.1

alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

7 x NCO: COBALT HEXAMMINE(III)(Non-functional Binders)(Non-covalent)

NCO.1: 1 residues within 4Å: Chain B: T.10 No protein-ligand interaction detected (PLIP) NCO.2: 4 residues within 4Å: Chain C: R.135, R.136, A.137, D.138 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.137, C:D.138, C:D.138 NCO.3: 4 residues within 4Å: Chain C: T.89, S.90, V.91, E.93 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.89, C:T.89, C:V.91, C:V.91, C:E.93, C:E.93 NCO.4: 8 residues within 4Å: Chain C: H.117, D.118, H.119, H.143, R.207, W.211, E.309 Ligands: UDP.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.117, C:D.118, C:H.143, C:R.207, C:E.309 NCO.7: 4 residues within 4Å: Chain D: R.135, R.136, A.137, D.138 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.135, D:A.137 NCO.8: 9 residues within 4Å: Chain D: G.18, H.117, D.118, H.119, R.207, W.211, E.309 Ligands: CL.6, UDP.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.118, D:H.119, D:H.143, D:R.207, D:E.309, D:E.309 NCO.9: 2 residues within 4Å: Chain D: D.104, N.105 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.104, D:D.104, D:N.105

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

UDP.5: 17 residues within 4Å: Chain C: G.16, C.17, G.18, K.21, R.49, S.52, H.53, R.207, K.212, C.277, Y.278, N.280, E.309, Y.310, T.311, E.314 Ligands: NCO.4 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.18, C:R.49, C:S.52, C:Y.278, C:Y.278, C:Y.278, C:Y.278, C:N.280, C:Y.310, C:T.311, C:E.314 Salt bridges: C:R.207, C:K.212, C:K.212 pi-Stacking: C:Y.278 UDP.10: 17 residues within 4Å: Chain D: G.16, C.17, G.18, R.49, S.52, H.53, R.207, K.212, C.277, Y.278, N.280, M.283, E.309, Y.310, T.311, E.314 Ligands: NCO.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.18, D:R.49, D:S.52, D:Y.278, D:Y.278, D:Y.278, D:N.280, D:E.309, D:Y.310, D:T.311, D:E.314 Salt bridges: D:R.207, D:K.212, D:K.212 pi-Stacking: D:Y.278

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

CL.6: 3 residues within 4Å: Chain D: H.117, H.143 Ligands: NCO.8 Ligand excluded by PLIP

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

EDO.11: 1 residues within 4Å: Chain D: K.249 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lariviere, L. et al., Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase. J.Mol.Biol. (2005)

Release Date

2005-08-30

Peptides

DNA alpha-glucosyltransferase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

DNA alpha-glucosyltransferase

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