SMTL ID : 8f93.1 (1 other biounit)

WDR5 covalently modified at Y228 by (R)-2-SF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x XKN: 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride(Covalent)

XKN.1: 11 residues within 4Å: Chain A: S.205, P.206, N.207, Y.210, K.232, V.250, L.270, Q.271 Chain B: R.163, P.206 Ligands: XKN.5 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.206, A:P.206, A:N.207, A:Y.210, A:K.232, A:V.250, A:L.270, A:L.270 Hydrogen bonds: A:N.207 Water bridges: A:R.163 pi-Cation interactions: B:R.163 XKN.5: 11 residues within 4Å: Chain A: V.250, K.254 Chain B: S.205, P.206, N.207, Y.210, K.232, V.250, L.270, Q.271 Ligands: XKN.1 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.206, B:N.207, B:Y.210, B:K.232, B:L.270 Hydrogen bonds: B:N.207

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: A.47, G.71, I.72, S.73, D.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.47, A:S.73 GOL.6: 5 residues within 4Å: Chain B: C.230, L.231, K.232, T.233, K.273 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.233, B:T.233, B:K.273 GOL.7: 6 residues within 4Å: Chain B: A.47, L.70, G.71, I.72, S.73, D.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.70, B:D.89 GOL.8: 3 residues within 4Å: Chain B: H.160, K.203 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.203, B:K.203

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

SO4.3: 6 residues within 4Å: Chain A: K.203, N.247, F.248, A.290, C.291 Ligands: CL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.247, A:C.291 Water bridges: A:K.203, A:K.203 Salt bridges: A:K.203 SO4.9: 6 residues within 4Å: Chain B: K.203, N.247, A.290, C.291 Ligands: GOL.8, CL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.247, B:C.291 Salt bridges: B:K.203

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: K.203 Ligands: SO4.3 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: K.203, N.247, F.248 Ligands: SO4.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes. Nat.Chem. (2023)

Release Date

2023-05-31

Peptides

WD repeat-containing protein 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

WD repeat-containing protein 5

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