SMTL ID : 6vdb.1

SETD2 in complex with a H3-variant super-substrate peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: K.144, G.145, W.146, I.186, H.187, Y.188, Y.189, R.209, F.210, M.211, N.212, H.213, Y.250, Q.260, K.261, C.262, F.263, C.264, L.273 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:W.146, A:W.146, A:W.146, A:Y.188, A:Y.188, A:N.212, A:H.213, A:H.213, A:Q.260, A:Q.260, A:F.263, A:C.264 Salt bridges: A:H.187

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

UNX.2: 4 residues within 4Å: Chain A: T.141, E.142, K.143, K.144 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: S.244, E.245 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: D.121, C.123, Q.132 Ligand excluded by PLIP UNX.5: 6 residues within 4Å: Chain A: C.123, S.124, N.125, R.126, R.127, Q.132 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: R.127, N.157, F.235 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: H.213, F.252, R.270, G.274 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: L.161, E.162, N.206 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: F.38, M.53, V.138 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: L.161, N.206, C.207 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: S.280, I.281, R.282 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: Y.180, N.183, N.185 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: Q.82, C.113, S.114, C.117 Ligand excluded by PLIP UNX.14: 5 residues within 4Å: Chain A: T.141, E.142, K.143, K.144, G.145 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain A: S.214, E.216, S.266 Ligands: UNX.16 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: K.144, C.264 Ligands: UNX.15 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: E.220, T.221, D.249 Chain B: N.11 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: Q.251, F.252, G.274 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: T.67, D.169 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: R.127, T.158, F.159 Ligand excluded by PLIP UNX.25: 1 residues within 4Å: Chain A: A.181 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.21: 5 residues within 4Å: Chain A: C.83, C.85, C.100, C.104 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.85, A:C.100, A:C.104 ZN.22: 5 residues within 4Å: Chain A: C.100, C.113, C.117, C.123 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.100, A:C.113, A:C.117, A:C.123 ZN.23: 5 residues within 4Å: Chain A: C.215, C.262, C.264, C.269, R.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.215, A:C.262, A:C.264, A:C.269

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.24: 7 residues within 4Å: Chain A: M.110, T.221, Q.222, K.223 Chain B: P.10, N.11, R.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuhmacher, M.K. et al., Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate. Commun Biol (2020)

Release Date

2020-01-29

Peptides

Histone-lysine N-methyltransferase SETD2: A
ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Histone-lysine N-methyltransferase SETD2

ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG

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