SMTL ID : 4bkx.1

The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: D.176, H.178, D.264 Ligands: ACT.2 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.176, B:D.176, B:H.178, B:D.264, ACT.2 ZN.9: 4 residues within 4Å: Chain D: D.176, H.178, D.264 Ligands: ACT.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.176, D:D.176, D:H.178, D:D.264, ACT.10

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

ACT.2: 8 residues within 4Å: Chain B: H.140, H.141, D.176, H.178, D.264, G.301, Y.303 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.301, B:Y.303, B:Y.303 Salt bridges: B:H.140, B:H.141, B:H.178 ACT.10: 8 residues within 4Å: Chain D: H.140, H.141, D.176, H.178, D.264, G.301, Y.303 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.301, D:Y.303 Salt bridges: D:H.140, D:H.141, D:H.178

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain B: D.174, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.174, B:D.176, B:S.197 K.4: 4 residues within 4Å: Chain B: F.187, T.190, V.193, Y.222 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.187 K.11: 6 residues within 4Å: Chain D: D.174, D.176, H.178, S.197, F.198, H.199 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.174, D:D.176, D:S.197 K.12: 4 residues within 4Å: Chain D: F.187, T.190, V.193, Y.222 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:F.187

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

SO4.5: 5 residues within 4Å: Chain B: R.270, Y.303, T.304, I.305, R.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.305, B:R.306 Salt bridges: B:R.270, B:R.306 SO4.6: 6 residues within 4Å: Chain A: K.146, Y.168, Y.169, K.172 Chain B: K.31 Ligands: SO4.7 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.168, A:Y.169 Salt bridges: A:K.146, A:K.172, B:K.31 SO4.7: 5 residues within 4Å: Chain A: K.146 Chain B: G.27, H.28, K.31 Ligands: SO4.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.27, B:G.27 Salt bridges: B:K.31, A:K.146 SO4.8: 3 residues within 4Å: Chain B: R.55, H.57, K.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.58 Salt bridges: B:R.55, B:H.57, B:K.58 SO4.13: 5 residues within 4Å: Chain D: R.270, Y.303, T.304, I.305, R.306 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.305, D:R.306 Salt bridges: D:R.270, D:R.306 SO4.14: 6 residues within 4Å: Chain C: K.146, Y.168, Y.169, K.172 Chain D: K.31 Ligands: SO4.15 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.31, C:K.146, C:K.172 SO4.15: 5 residues within 4Å: Chain C: K.146 Chain D: G.27, H.28, K.31 Ligands: SO4.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.27, D:G.27 Salt bridges: D:K.31, C:K.146 SO4.16: 3 residues within 4Å: Chain D: R.55, H.57, K.58 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.58 Salt bridges: D:R.55, D:H.57, D:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Millard, C.J. et al., Class I Hdacs Share a Common Mechanism of Regulation by Inositol Phosphates. Mol.Cell (2013)

Release Date

2013-07-03

Peptides

METASTASIS-ASSOCIATED PROTEIN MTA1: AC
HISTONE DEACETYLASE 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

METASTASIS-ASSOCIATED PROTEIN MTA1

HISTONE DEACETYLASE 1

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