SMTL ID : 6q3m.1 (3 other biounits)

Structure of CHD4 PHD2 - tandem chromodomains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.23, T.25, C.26, S.28, C.49, R.51, C.52 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.23, A:C.26, A:C.49, A:C.52 ZN.2: 5 residues within 4Å: Chain A: C.11, V.13, C.14, H.31, C.34 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.14, A:H.31, A:C.34

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: Q.134, R.135, K.136, N.137, D.138, M.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.135, A:N.137 PGE.4: 6 residues within 4Å: Chain A: W.69, R.97, P.98, D.140, E.141, P.142 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.98 PGE.5: 8 residues within 4Å: Chain A: F.103, C.114, S.115, W.116, E.169, R.170, Y.174 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.116, A:W.116, A:R.170, A:R.170, A:Y.174 Water bridges: A:S.115

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: R.185, I.186, F.226, S.229, Y.230, H.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.186, A:F.226 EDO.7: 5 residues within 4Å: Chain A: R.51, E.123, L.124, Q.127 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51, A:R.51, A:E.123 EDO.8: 3 residues within 4Å: Chain A: R.12, V.13, K.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.15 EDO.9: 6 residues within 4Å: Chain A: C.26, S.28, R.51, C.52, L.124 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.51, A:R.51 EDO.10: 5 residues within 4Å: Chain A: K.68, Q.101, W.116 Ligands: PGE.5, EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.68, A:Q.101 EDO.11: 5 residues within 4Å: Chain A: E.99, E.119, L.120, E.123 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.99 Water bridges: A:E.119, A:E.123, A:E.123 EDO.12: 9 residues within 4Å: Chain A: R.12, V.13, Y.30, P.50, R.51, L.120, E.123 Ligands: EDO.7, EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.51 EDO.13: 5 residues within 4Å: Chain A: Q.101, W.116, V.117, S.118 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: L.65, I.66, W.67, Y.133, N.137, P.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 4 residues within 4Å: Chain A: S.190, D.192, H.198, W.213 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mancini, E.J. et al., Structure of histone readers. To Be Published

Release Date

2019-12-25

Peptides

Chromodomain-helicase-DNA-binding protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chromodomain-helicase-DNA-binding protein 4

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