SMTL ID : 4fmu.1

Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.66, C.68, C.83, C.87 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.68, A:C.83, A:C.87 ZN.2: 5 residues within 4Å: Chain A: C.83, C.96, C.100, C.106 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.100, A:C.106 ZN.3: 4 residues within 4Å: Chain A: C.198, C.245, C.247, C.252 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.245, A:C.247, A:C.252

1 x 0UM: (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid(Non-covalent)

0UM.4: 21 residues within 4Å: Chain A: K.127, G.128, W.129, Y.146, I.169, H.170, Y.171, Y.172, R.192, F.193, M.194, N.195, H.196, F.231, Y.233, Q.243, K.244, C.245, F.246, C.247, L.256 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.146, A:F.231, A:Y.233 Hydrogen bonds: A:W.129, A:W.129, A:Y.171, A:Y.171, A:N.195, A:N.195, A:H.196, A:H.196, A:Q.243, A:Q.243, A:F.246 Water bridges: A:R.192 Salt bridges: A:H.170

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

UNX.5: 2 residues within 4Å: Chain A: Y.163, Y.171 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: D.179, E.180 No protein-ligand interaction detected (PLIP) UNX.7: 3 residues within 4Å: Chain A: E.203, T.204 Ligands: UNX.8 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: T.204, D.232 Ligands: UNX.7, UNX.15 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: R.113, K.114, Q.115 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Chain A: R.113 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: K.177, N.178 No protein-ligand interaction detected (PLIP) UNX.12: 1 residues within 4Å: Chain A: N.210 No protein-ligand interaction detected (PLIP) UNX.13: 1 residues within 4Å: Chain A: K.177 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: E.44, K.114 No protein-ligand interaction detected (PLIP) UNX.15: 6 residues within 4Å: Chain A: M.174, F.231, Y.233, Q.234 Ligands: UNX.8, UNX.17 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: F.235, Q.236 Ligands: UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 5 residues within 4Å: Chain A: M.174, A.175, Q.234 Ligands: UNX.15, UNX.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, W. et al., Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2. J.Am.Chem.Soc. (2012)

Release Date

2012-09-05

Peptides

Histone-lysine N-methyltransferase SETD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETD2

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