SMTL ID : 6lzy.1

Structure of Phytolacca americana UGT3 with 18-crown-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x BR: BROMIDE ION(Non-covalent)

BR.1: 5 residues within 4Å: Chain A: H.201, E.248, P.249, N.250, Y.251 Ligand excluded by PLIP BR.2: 3 residues within 4Å: Chain A: K.420, N.423, Q.424 Ligand excluded by PLIP BR.9: 6 residues within 4Å: Chain B: H.201, E.248, P.249, N.250, Y.251, I.425 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain B: N.423, Q.424 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: R.225, L.226, I.229 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.225 EDO.4: 3 residues within 4Å: Chain A: P.148, W.149, L.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.149 EDO.5: 5 residues within 4Å: Chain A: M.145, F.146, A.413, E.414 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: L.50, I.266, P.268, L.271, C.272, V.483, Y.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.268 EDO.10: 6 residues within 4Å: Chain B: P.148, T.151, L.228, E.231, S.232, K.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.151, B:L.228 EDO.11: 9 residues within 4Å: Chain B: M.145, H.165, T.167, L.172, L.175, K.230 Ligands: EDO.12, EDO.13, EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.230, B:K.230 EDO.12: 6 residues within 4Å: Chain B: L.175, P.211, A.413, E.414 Ligands: EDO.11, EDO.13 No protein-ligand interaction detected (PLIP) EDO.13: 7 residues within 4Å: Chain B: M.145, R.225, L.226, I.229 Ligands: EDO.11, EDO.12, EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.222 EDO.14: 6 residues within 4Å: Chain B: H.40, F.146, A.413, E.414 Ligands: EDO.11, EDO.15 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: F.146, R.225, R.439 Ligands: EDO.13, EDO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.225 EDO.16: 5 residues within 4Å: Chain B: R.54, S.494, I.497, E.498, R.501 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.54, B:E.498, B:E.498, B:R.501 EDO.17: 8 residues within 4Å: Chain B: L.50, I.266, P.268, V.269, L.271, C.272, V.483, S.489 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.269, B:L.271, B:S.489 EDO.18: 5 residues within 4Å: Chain B: A.37, H.38, G.39, H.40, T.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.38, B:G.39, B:H.40

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: E.258 Chain B: E.258 Ligands: O4B.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.258

1 x O4B: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE(Non-covalent)

O4B.8: 15 residues within 4Å: Chain A: L.180, Y.181, L.198, K.257, E.258, L.259, G.260 Chain B: L.180, Y.181, L.198, K.257, E.258, L.259, G.260 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maharjan, R. et al., Crown-ether-mediated crystal structures of the glycosyltransferase PaGT3 from Phytolacca americana. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-06-10

Peptides

Glycosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycosyltransferase

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