SMTL ID : 5grq.1

Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-2-2-mer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: H.42, S.43, A.85 Chain B: C.4, K.6 Ligands: ZN.8, CL.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.43 Salt bridges: A:H.42, B:K.6 Hydrophobic interactions: B:K.6 ACT.2: 4 residues within 4Å: Chain A: H.27, E.29 Chain C: L.22 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.27 ACT.10: 7 residues within 4Å: Chain A: C.4, K.6 Chain B: H.42, S.43, A.85 Ligands: CL.6, ZN.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.43 Salt bridges: B:H.42, A:K.6 Hydrophobic interactions: A:K.6 Water bridges: A:K.6 ACT.11: 4 residues within 4Å: Chain A: G.1 Chain B: E.50, H.83 Ligands: ZN.13 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.83 ACT.18: 5 residues within 4Å: Chain C: D.4, D.6, D.9, R.15 Ligands: ZN.19 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.15, C:K.18, C:K.18 Salt bridges: C:R.15, C:K.18

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.50 Chain B: K.2 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.2, B:K.2

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

CL.4: 7 residues within 4Å: Chain A: E.50, H.83 Chain B: G.1, K.2 Ligands: GOL.3, CL.5, ZN.7 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: F.45, E.50, H.83 Chain B: K.2 Ligands: CL.4, ZN.7 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: C.4, K.6, L.7 Chain B: H.42 Ligands: ACT.10, ZN.12 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: H.42 Chain B: C.4, K.6, L.7 Ligands: ACT.1, ZN.8 Ligand excluded by PLIP

11 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: F.45, E.50, H.83 Ligands: CL.4, CL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.50, A:E.50, A:H.83 ZN.8: 6 residues within 4Å: Chain A: H.42, S.43 Chain B: C.4, K.6 Ligands: ACT.1, CL.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.42, B:C.4 ZN.9: 3 residues within 4Å: Chain A: H.27, E.29 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.27, A:E.29, A:E.29 ZN.12: 6 residues within 4Å: Chain A: C.4, K.6 Chain B: H.42, S.43 Ligands: CL.6, ACT.10 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.42, A:C.4, ACT.10 ZN.13: 4 residues within 4Å: Chain A: G.1 Chain B: E.50, H.83 Ligands: ACT.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.50, B:E.50, B:H.83, ACT.11 ZN.14: 2 residues within 4Å: Chain A: C.77 Chain C: E.24 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:E.24, C:E.24, A:C.77, H2O.1, H2O.14 ZN.16: 2 residues within 4Å: Chain B: H.27, E.29 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.27, B:E.29, B:E.29 ZN.17: 3 residues within 4Å: Chain B: C.77, T.78 Chain D: E.24 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:E.24, D:E.24, B:C.77, H2O.8, H2O.16 ZN.19: 4 residues within 4Å: Chain C: D.4, D.6, D.9 Ligands: ACT.18 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.4, C:D.4, C:D.6, C:D.9, ACT.18 ZN.20: 3 residues within 4Å: Chain A: Q.23 Chain C: D.7, D.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.7, H2O.1, H2O.13, H2O.13 ZN.21: 1 residues within 4Å: Chain C: E.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.13, C:E.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H., Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide. To be published

Release Date

2017-09-27

Peptides

Death domain-associated protein 6: AB
Transcriptional regulator ATRX: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Death domain-associated protein 6

Transcriptional regulator ATRX