SMTL ID : 5i3l.1

DPF3b in complex with H3K14ac peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.9, C.12, N.19, H.39, C.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.12, A:H.39, A:C.42 ZN.2: 4 residues within 4Å: Chain A: C.31, C.34, C.60, C.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.31, A:C.34, A:C.60, A:C.63 ZN.3: 4 residues within 4Å: Chain A: C.66, C.69, H.89, C.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.89, A:C.92 ZN.4: 4 residues within 4Å: Chain A: C.81, C.84, C.107, C.110 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.81, A:C.84, A:C.107, A:C.110 ZN.22: 4 residues within 4Å: Chain B: C.9, C.12, H.39, C.42 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.9, B:C.12, B:H.39, B:C.42 ZN.23: 4 residues within 4Å: Chain B: C.31, C.34, C.60, C.63 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.31, B:C.34, B:C.60, B:C.63 ZN.24: 4 residues within 4Å: Chain B: C.66, C.69, H.89, C.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.66, B:C.69, B:H.89, B:C.92 ZN.25: 4 residues within 4Å: Chain B: C.81, C.84, C.107, C.110 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.81, B:C.84, B:C.107, B:C.110

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

EDO.5: 6 residues within 4Å: Chain A: E.27, T.50, E.51, K.54 Chain B: W.111, L.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.27, A:E.51, A:E.51

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

UNX.6: 4 residues within 4Å: Chain A: S.104, W.105, S.106 Chain B: F.45 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: E.26, E.27 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: P.101, E.102, G.103 Chain B: K.21 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: N.48, E.51, A.52 Ligand excluded by PLIP UNX.10: 3 residues within 4Å: Chain A: F.80, D.85 Chain C: R.2 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: I.67, L.68 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain A: F.11, K.21, C.42, Q.44 Chain C: T.11 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: F.11 Chain C: G.12, G.13 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: G.15, S.16, N.17, M.18 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: S.30, V.53 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: T.55, R.86 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: Q.44, T.46 Chain B: D.82, S.104 Ligand excluded by PLIP UNX.18: 5 residues within 4Å: Chain A: Q.44, F.45, T.46, M.49 Ligands: UNX.19 Ligand excluded by PLIP UNX.19: 5 residues within 4Å: Chain A: T.46, M.49, D.82 Chain B: T.46 Ligands: UNX.18 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: S.16, E.27, L.28 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain A: I.4, P.5, N.7 Ligand excluded by PLIP UNX.26: 3 residues within 4Å: Chain B: V.29, S.30 Ligands: UNX.38 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain B: N.6, N.7 Ligand excluded by PLIP UNX.29: 4 residues within 4Å: Chain B: N.19, S.22, E.26, T.41 Ligand excluded by PLIP UNX.30: 3 residues within 4Å: Chain B: P.5, S.30, C.31 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain B: N.6, R.36 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: D.85 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: L.78, F.80 Ligand excluded by PLIP UNX.34: 3 residues within 4Å: Chain B: W.105, S.106, W.111 Ligand excluded by PLIP UNX.35: 1 residues within 4Å: Chain B: D.33 Ligand excluded by PLIP UNX.36: 4 residues within 4Å: Chain B: E.27, L.28, V.29, K.54 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain B: F.11, K.21, C.42 Ligand excluded by PLIP UNX.38: 4 residues within 4Å: Chain B: V.53, Y.56, W.58 Ligands: UNX.26 Ligand excluded by PLIP UNX.39: 3 residues within 4Å: Chain B: Y.56, K.57, I.67 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain B: N.94, P.95 Ligand excluded by PLIP UNX.41: 4 residues within 4Å: Chain B: R.86, C.110, L.113 Ligands: UNX.42 Ligand excluded by PLIP UNX.42: 4 residues within 4Å: Chain B: A.52, T.55, L.113 Ligands: UNX.41 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.28: 2 residues within 4Å: Chain B: F.80, D.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.80, B:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Crystal structure of DPF3b in complex with an acetylated histone peptide. J.Struct.Biol. (2016)

Release Date

2016-02-24

Peptides

Zinc finger protein DPF3: AB
H3K14ac peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Zinc finger protein DPF3

H3K14ac peptide

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