SMTL ID : 6oi0.1

Crystal structure of human WDR5 in complex with L-arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x ARG: ARGININE(Non-covalent)

ARG.1: 8 residues within 4Å: Chain A: S.28, S.70, F.112, Y.239, C.240, F.242, I.284 Ligands: GOL.7 9 PLIP interactions: 3 Ligand-Ligand interactions, 6 interactions with chain A Water bridges: R.1, R.1, R.1 Hydrophobic interactions: A:F.112, A:I.284 Hydrogen bonds: A:S.70, A:S.70, A:C.240 Salt bridges: A:D.71

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

SO4.2: 2 residues within 4Å: Chain A: H.157, K.200 11 PLIP interactions: 11 interactions with chain A Water bridges: A:K.31, A:K.31, A:N.115, A:H.157, A:K.200, A:K.200, A:K.200, A:N.244, A:N.244 Salt bridges: A:H.157, A:K.200 SO4.3: 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:D.281, A:E.301

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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.5: 10 residues within 4Å: Chain A: G.172, L.173, C.174, L.188, D.190, V.196, A.210, T.212, K.218, W.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.174, A:L.188, A:W.220 Water bridges: A:D.190 GOL.6: 5 residues within 4Å: Chain A: L.122, I.134, K.144, T.179, A.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144, A:K.144 GOL.7: 6 residues within 4Å: Chain A: S.70, D.86, Y.110, F.112, F.128 Ligands: ARG.1 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: R.1, R.1, A:S.70, A:D.86

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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