SMTL ID : 5zba.1

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 23 residues within 4Å: Chain A: A.94, D.95, S.96, S.110, L.111, L.112, R.113, F.139, A.140, R.141, Q.143, N.144, Y.146, E.156, K.157, H.158, V.159, L.160, L.165, W.168, W.169, R.171 Ligands: IOD.28 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.160 Hydrogen bonds: A:A.94, A:D.95, A:S.96, A:L.112, A:R.113, A:Q.143, A:E.156, A:H.158, A:W.168 Salt bridges: A:R.113, A:R.171 pi-Stacking: A:H.158, A:H.158

37 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: H.55, D.411 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: N.237 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: L.297 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: H.101, L.102, E.156 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: L.297, W.301 Ligands: IOD.16 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: R.163, C.212, E.216 Chain D: R.96 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: H.242, Q.243 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: R.113, L.114, N.117 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: A.41, P.47 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: P.63 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: R.253 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: D.261, D.262 Chain C: S.58 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: E.77, K.425, I.428 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Ligands: IOD.7 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: D.161, D.162, R.314 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: T.83, R.129 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain B: L.40, V.141, R.182 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain C: R.84, F.85 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain B: T.83 Chain C: K.126 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain C: R.50 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain C: R.64, K.65 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain C: S.87, S.88 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain C: R.53 Chain D: R.40 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain C: R.117, V.118, T.119 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain C: Q.56, E.60 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: A.94 Chain C: K.57 Ligands: COA.1 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain C: T.46, T.119, Q.121 Chain D: S.48 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain A: N.429 Chain C: R.54 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain C: R.54 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain C: R.129 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain C: R.64 Chain D: T.31 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain D: L.50, E.53 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain C: Q.121, K.122 Chain D: S.48, L.50 Ligand excluded by PLIP IOD.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.37: 1 residues within 4Å: Chain D: R.37 Ligand excluded by PLIP IOD.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Cell (2018)

Release Date

2018-07-25

Peptides

DNA damage response protein Rtt109, putative: A
Histone chaperone asf1: B
Histone H3: C
Histone H4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DNA damage response protein Rtt109, putative

Histone chaperone asf1

Histone H3

Histone H4

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