SMTL ID : 6v63.1 (1 other biounit)

SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: T.12, N.13, K.19 Chain B: N.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:N.13, A:K.19 GOL.3: 3 residues within 4Å: Chain B: K.128, F.173, W.174 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.128

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 17 residues within 4Å: Chain B: R.77, E.105, E.106, F.108, P.182, T.255, R.256, D.277, M.278, C.279, N.280, H.281, Y.315, S.327, F.329, F.331 Ligands: EDO.20 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:F.108, B:F.108, B:N.280, B:H.281, B:H.281, B:Y.315 Water bridges: B:E.106, B:E.106, B:E.106, B:D.186, B:T.255, B:T.255, B:S.327, B:G.328 Salt bridges: B:R.77, B:R.256 pi-Stacking: B:F.329, B:F.329

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

EDO.4: 12 residues within 4Å: Chain B: S.319, N.320, A.321, D.337, R.338, V.339, L.469, G.472, E.473, I.476 Ligands: EDO.6, EDO.9 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain B: D.207, A.321, E.322, I.325, H.326 Ligands: EDO.6, EDO.9 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain B: Q.203, A.204, A.321, K.340, E.473 Ligands: EDO.4, EDO.5, EDO.9 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: A.362, A.381, I.410 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: D.115, I.116, K.117, D.304, F.305, R.306 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain B: S.319, E.322, R.338, V.339, K.340 Ligands: EDO.4, EDO.5, EDO.6 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: L.454, H.457, D.458, L.459, K.464 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: Y.4, P.5, I.6 Chain B: Q.259, I.260, P.261, V.268 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: D.337, F.374, G.472, E.475, I.476 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: P.43, E.48, E.51, H.206, F.209, S.210, K.213 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: R.63, K.64, Q.66 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: I.27, Q.66, Y.223, S.240, F.241, T.242 Ligands: EDO.18 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: F.330, V.461, K.464, M.465, K.468 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.402, G.403, D.404, S.405, A.406, R.409 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: Y.223, I.226, Q.227, L.237, K.238, F.241 Ligands: EDO.15 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: L.343, G.344, F.390, R.435 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.77, G.107, F.108 Ligands: SAH.2 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: D.404 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: E.376, P.377, S.483, N.487 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: A.118, E.119, E.120 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.22: 4 residues within 4Å: Chain B: F.370, A.371, S.380, Q.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.371, B:S.380 Water bridges: B:S.380, B:A.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. J.Biol.Chem. (2020)

Release Date

2020-01-22

Peptides

Actin, cytoplasmic 1: A
Actin-histidine N-methyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
A

Actin, cytoplasmic 1

Actin-histidine N-methyltransferase

Related Entries With Identical Sequence