SMTL ID : 4i51.1

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-1-mer

Ligands

2 x THR- LYS- GLN- THR- ALA- ARG- LDH- SER- THR: H3K9 NE-ALLYL PEPTIDE(Non-covalent)

THR-LYS-GLN-THR-ALA-ARG-LDH-SER-THR.1: 22 residues within 4Å: Chain A: Y.175, D.182, A.185, D.186, R.188, D.191, S.192, L.194, F.195, D.196, N.199, I.219, H.221, P.229, R.231, F.260, A.262, R.265, F.266, I.269, K.270 Ligands: SAH.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.195, A:P.229, A:F.266, A:I.269, A:K.270 Hydrogen bonds: A:D.182, A:D.182, A:D.182, A:D.186, A:D.186, A:D.191, A:S.192, A:L.194, A:D.196, A:N.199, A:R.231, A:R.231, A:A.262, A:R.265 Water bridges: A:Y.175, A:L.194, A:D.196, A:F.266 Salt bridges: A:D.182, A:D.186, A:D.196 THR-LYS-GLN-THR-ALA-ARG-LDH-SER-THR.2: 21 residues within 4Å: Chain B: Y.175, D.182, A.185, D.186, R.188, D.191, S.192, L.194, F.195, D.196, C.206, I.219, H.221, F.260, D.261, A.262, R.265, F.266, I.269, K.270 Ligands: SAH.18 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.195, B:F.195, B:F.260, B:F.266, B:I.269, B:K.270 Hydrogen bonds: B:D.182, B:A.185, B:D.186, B:D.191, B:D.191, B:S.192, B:L.194, B:D.196, B:A.262, B:R.265 Water bridges: B:Y.175 Salt bridges: B:D.182, B:D.186, B:D.196

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

SAH.3: 19 residues within 4Å: Chain A: M.156, G.157, W.158, S.192, Y.193, R.217, F.218, I.219, N.220, H.221, F.266, W.267, K.270, F.274, S.275, C.276, R.277, C.278 Ligands: THR-LYS-GLN-THR-ALA-ARG-LDH-SER-THR.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:M.156, A:W.158, A:W.158, A:Y.193, A:H.221, A:H.221, A:R.277 Water bridges: A:R.277 SAH.18: 17 residues within 4Å: Chain B: M.156, G.157, W.158, S.192, Y.193, R.217, F.218, I.219, N.220, H.221, F.266, F.274, S.275, C.276, R.277, C.278 Ligands: GLN-THR-ALA-ARG-LDH-SER-THR.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:M.156, B:W.158, B:W.158, B:S.192, B:N.220, B:H.221, B:H.221, B:R.277

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: C.82, C.95, C.125, C.129 Ligands: ZN.5, ZN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.82, A:C.95, A:C.125, A:C.129 ZN.5: 6 residues within 4Å: Chain A: C.88, C.125, C.131, C.135 Ligands: ZN.4, ZN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.88, A:C.125, A:C.131, A:C.135 ZN.6: 6 residues within 4Å: Chain A: C.82, C.84, C.88, C.93 Ligands: ZN.4, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.82, A:C.84, A:C.88, A:C.93 ZN.7: 4 residues within 4Å: Chain A: C.223, C.276, C.278, C.283 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.223, A:C.276, A:C.278, A:C.283 ZN.19: 6 residues within 4Å: Chain B: C.82, C.95, C.125, C.129 Ligands: ZN.20, ZN.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.82, B:C.95, B:C.125, B:C.129 ZN.20: 7 residues within 4Å: Chain B: C.82, C.88, C.125, C.131, C.135 Ligands: ZN.19, ZN.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.88, B:C.125, B:C.131, B:C.135 ZN.21: 6 residues within 4Å: Chain B: C.82, C.84, C.88, C.93 Ligands: ZN.19, ZN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.82, B:C.84, B:C.88, B:C.93 ZN.22: 4 residues within 4Å: Chain B: C.223, C.276, C.278, C.283 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.223, B:C.276, B:C.278, B:C.283

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: N.64, I.72, R.74 Chain B: R.74 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:R.74, B:R.74, A:V.66, A:R.74 Hydrogen bonds: A:R.74 GOL.9: 5 residues within 4Å: Chain A: C.84, I.85, D.86, S.90, N.92 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.85, A:D.86, A:D.86, A:S.90, A:N.92 Water bridges: A:C.88, A:S.90 GOL.23: 5 residues within 4Å: Chain A: R.74 Chain B: N.64, I.72, R.74, L.179 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.74 Water bridges: B:Q.63, B:N.64, B:V.66, A:R.74

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

UNX.10: 1 residues within 4Å: Chain A: F.123 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: W.132, N.134 No protein-ligand interaction detected (PLIP) UNX.12: 1 residues within 4Å: Chain A: Q.97 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: Y.151, Q.257 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: L.163, G.255 No protein-ligand interaction detected (PLIP) UNX.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Chain A: P.119 No protein-ligand interaction detected (PLIP) UNX.17: 4 residues within 4Å: Chain A: V.66, P.69, M.70, N.71 No protein-ligand interaction detected (PLIP) UNX.24: 2 residues within 4Å: Chain B: R.74, H.236 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, K. et al., Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2012-12-19

Peptides

Histone-lysine N-methyltransferase EHMT1: AB
UNKNOWN PEPTIDE: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
K

Histone-lysine N-methyltransferase EHMT1

UNKNOWN PEPTIDE

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