SMTL ID : 5vc8.1

Crystal structure of the WHSC1 PWWP1 domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x DC- DT- DN: DNA (5'-D(P*CP*TP*(DN))-3')(Non-functional Binders)

DC-DT-DN.1: 6 residues within 4Å: Chain C: A.2, G.3, A.4, T.5 Chain D: A.8, T.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.95, A:A.96

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

UNX.2: 5 residues within 4Å: Chain A: K.42, Q.52 Chain B: V.21 Ligands: UNX.18, UNX.25 Ligand excluded by PLIP UNX.3: 4 residues within 4Å: Chain A: V.21, S.22 Chain B: K.44 Ligands: UNX.28 Ligand excluded by PLIP UNX.4: 1 residues within 4Å: Chain A: E.114 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: A.111, E.114, M.115 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: G.77, E.78, G.79 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: E.82, C.85, Q.86 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: G.59, D.60, Q.112 Ligands: UNX.12 Ligand excluded by PLIP UNX.9: 5 residues within 4Å: Chain A: K.20, G.23, K.100, L.101 Ligands: UNX.11 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: K.90, Q.91, A.92, K.98 Ligand excluded by PLIP UNX.11: 5 residues within 4Å: Chain A: K.20, Y.24, K.100, L.101 Ligands: UNX.9 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain A: G.59, D.60, A.61, P.62 Ligands: UNX.8 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: D.15, L.16, R.131 Ligands: UNX.14 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: L.16, A.74 Ligands: UNX.13, UNX.15 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: Y.11, A.74 Ligands: UNX.14 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Chain A: Y.40 Ligand excluded by PLIP UNX.17: 3 residues within 4Å: Chain A: F.68, E.69, K.70 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain A: K.44 Chain B: V.21, S.22 Ligands: UNX.2 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: A.65, W.66, I.67 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: K.108, L.109, R.110, A.111, Q.112 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: N.12, D.15 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain B: G.77, E.78, G.79 Ligands: UNX.24 Ligand excluded by PLIP UNX.23: 1 residues within 4Å: Chain B: K.134 Ligand excluded by PLIP UNX.24: 4 residues within 4Å: Chain B: G.77, E.78, E.121 Ligands: UNX.22 Ligand excluded by PLIP UNX.25: 4 residues within 4Å: Chain A: W.66 Chain B: V.21, A.65 Ligands: UNX.2 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain B: K.132 Ligands: UNX.39 Ligand excluded by PLIP UNX.27: 1 residues within 4Å: Chain B: L.102 Ligand excluded by PLIP UNX.28: 5 residues within 4Å: Chain A: V.21 Chain B: K.42, Q.52, W.66 Ligands: UNX.3 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain B: K.42, L.43, Q.46 Ligand excluded by PLIP UNX.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.31: 4 residues within 4Å: Chain B: S.39, T.41, K.42 Ligands: UNX.32 Ligand excluded by PLIP UNX.32: 3 residues within 4Å: Chain B: L.37, S.39 Ligands: UNX.31 Ligand excluded by PLIP UNX.33: 4 residues within 4Å: Chain B: E.129, K.132, A.133 Ligands: UNX.39 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain B: S.106, G.107, K.108, L.109 Ligand excluded by PLIP UNX.35: 1 residues within 4Å: Chain B: E.122 Ligand excluded by PLIP UNX.36: 1 residues within 4Å: Chain B: K.132 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain B: G.59, D.60, A.61 Ligand excluded by PLIP UNX.38: 3 residues within 4Å: Chain B: E.114, I.117, V.118 Ligand excluded by PLIP UNX.39: 4 residues within 4Å: Chain B: K.132, A.133 Ligands: UNX.26, UNX.33 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain B: L.101, L.102, K.103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Histone and DNA binding ability studies of the NSD subfamily of PWWP domains. Biochem.Biophys.Res.Commun. (2021)

Release Date

2017-06-28

Peptides

Histone-lysine N-methyltransferase NSD2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase NSD2

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