SMTL ID : 6oi2.1

Crystal structure of human WDR5 in complex with symmetric dimethyl-L-arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: H.157, K.200 7 PLIP interactions: 7 interactions with chain A Water bridges: A:N.115, A:N.115, A:N.115, A:K.200, A:K.200 Salt bridges: A:H.157, A:K.200 SO4.2: 1 residues within 4Å: Chain A: K.88 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.88 SO4.3: 4 residues within 4Å: Chain A: Y.207, L.219, K.229, Q.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.229, A:Q.268, A:Q.268

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.122, L.143, K.144, T.179, A.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144, A:T.179 GOL.5: 4 residues within 4Å: Chain A: A.21, G.22, K.49, F.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.49 GOL.6: 5 residues within 4Å: Chain A: Y.239, D.281, L.300, E.301, N.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.239, A:E.301 Water bridges: A:N.302

1 x 2MR: N3, N4-DIMETHYLARGININE(Non-covalent)

2MR.7: 10 residues within 4Å: Chain A: S.28, S.70, D.71, F.112, S.197, F.198, Y.239, C.240, F.242, I.284 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:I.284 Hydrogen bonds: A:S.70, A:S.70, A:C.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorton, B.M. et al., A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5. Biochemistry (2020)

Release Date

2020-04-01

Peptides

WD repeat-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WD repeat-containing protein 5

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