SMTL ID : 3qwp.1

Crystal structure of SET and MYND domain containing 3; Zinc finger MYND domain-containing protein 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.63, C.66, H.84, C.88 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:H.84, A:C.88 ZN.2: 4 residues within 4Å: Chain A: C.50, C.53, C.72, C.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.50, A:C.53, A:C.72, A:C.76 ZN.3: 4 residues within 4Å: Chain A: C.209, C.262, C.264, C.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.209, A:C.262, A:C.264, A:C.267

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 17 residues within 4Å: Chain A: R.15, G.16, N.17, Y.125, E.131, N.133, C.181, N.182, S.203, L.204, L.205, N.206, H.207, Y.240, Y.258, F.260 Ligands: GOL.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.15, A:N.17, A:E.131, A:N.133, A:N.133, A:N.206, A:N.206, A:H.207, A:H.207 Water bridges: A:R.15, A:Y.125, A:Y.125, A:S.203, A:D.263 pi-Stacking: A:F.260, A:F.260

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: N.182, S.183, F.184, S.203, I.238, Y.240, Y.258 Ligands: SAM.4, GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.203 Water bridges: A:S.183, A:Y.240, A:Y.240 GOL.6: 9 residues within 4Å: Chain A: S.183, F.184, T.185, I.215, F.217, I.238, Y.240 Ligands: GOL.5, GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.185, A:T.185, A:T.185 Water bridges: A:C.239 GOL.7: 10 residues within 4Å: Chain A: E.190, M.191, K.298, D.333, D.337, Y.359, V.369, V.372, Q.373, K.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.298, A:K.298, A:D.333 GOL.8: 5 residues within 4Å: Chain A: F.152, Q.153, I.160, Q.161, L.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.153 Water bridges: A:Q.153, A:I.160 GOL.9: 3 residues within 4Å: Chain A: R.141, I.180, Q.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.141, A:R.141, A:I.180 Water bridges: A:S.183, A:S.183 GOL.10: 6 residues within 4Å: Chain A: P.82, D.83, F.111, K.112, D.115, G.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.83, A:F.111 GOL.11: 6 residues within 4Å: Chain A: C.239, L.241, M.243, H.367 Ligands: GOL.6, GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.243, A:H.367 GOL.12: 8 residues within 4Å: Chain A: C.187, M.191, I.215, V.216, H.367, P.368, V.369 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dombrovski, L. et al., The Crystal Structure of human Histone-lysine N-methyltransferase SMYD3. To be Published

Release Date

2011-04-06

Peptides

SET and MYND domain-containing protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SET and MYND domain-containing protein 3

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