SMTL ID : 6cbx.2 (1 other biounit)

Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.53, C.56, C.75, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.56, A:C.75, A:C.79 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, H.87, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.87, A:C.91 ZN.3: 4 residues within 4Å: Chain A: C.210, C.263, C.265, C.268 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.210, A:C.263, A:C.265, A:C.268

1 x EW1: [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl )-1H-pyrrol-3-yl]methanone(Non-covalent)

EW1.4: 17 residues within 4Å: Chain A: G.17, K.18, E.136, H.138, C.182, N.183, G.184, F.185, A.204, N.207, H.208, Y.241, Y.259, F.261, T.262, E.264 Ligands: UNX.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.185, A:A.204, A:Y.241, A:Y.259 Hydrogen bonds: A:H.208, A:H.208 pi-Stacking: A:Y.259, A:F.261, A:F.261

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

CL.5: 3 residues within 4Å: Chain A: I.242, D.243, R.254 Ligand excluded by PLIP

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

EDO.6: 7 residues within 4Å: Chain A: R.68, W.84, K.88, C.91, S.92, P.93, H.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.68, A:S.92 EDO.7: 2 residues within 4Å: Chain A: H.159, S.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.162, A:S.162

5 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 3 residues within 4Å: Chain A: R.20, E.136 Ligands: EW1.4 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: E.414, G.418, K.419 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: F.13, C.14 No protein-ligand interaction detected (PLIP) UNX.11: 5 residues within 4Å: Chain A: P.103, S.104, V.107, D.153, A.156 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain A: T.124, P.125, S.126 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

ZENG, H. et al., Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497. to be published

Release Date

2018-03-14

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

N-lysine methyltransferase SMYD2

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