SMTL ID : 8sr6.1

Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 14 residues within 4Å: Chain A: L.44, G.49, R.50, S.90, Y.91, R.110, Y.111, I.112, N.113, F.114, Y.152, Y.163, Y.164, L.166 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.50, A:R.50, A:Y.91, A:Y.91, A:F.114, A:Y.163, A:Y.164, A:Y.164 Water bridges: A:N.19, A:S.90, A:Y.163, A:L.166 pi-Stacking: A:Y.163, A:Y.163

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: G.145, G.169, G.171, W.172, L.173, F.178 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.145, A:W.172, A:L.173 Water bridges: A:G.169, A:G.171, A:G.171

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

PEG.3: 5 residues within 4Å: Chain A: R.161, Y.162, Y.164, H.285, R.326 No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: P.394, D.395, G.439, L.440, H.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.394 EDO.5: 8 residues within 4Å: Chain A: F.114, D.116, A.159, S.160, Y.163, Y.164, F.165, H.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.164, A:H.324 EDO.6: 6 residues within 4Å: Chain A: N.120, N.141, I.142, K.143, Q.146, P.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.120, A:K.143, A:Q.146 EDO.7: 4 residues within 4Å: Chain A: V.71, R.98, K.131, V.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.131 EDO.8: 8 residues within 4Å: Chain A: S.292, V.323, H.324, D.325, K.329, T.330, F.331, N.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.325, A:N.334 EDO.9: 5 residues within 4Å: Chain A: M.12, L.13, H.16, I.17, D.18 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: R.213, Y.219 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: E.189, Q.190, P.192, R.213 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.189, A:Q.190 EDO.12: 2 residues within 4Å: Chain A: G.169, D.233 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain A: N.19, M.20, Y.91, A.103, R.110, Y.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.103, A:R.110, A:R.110 Water bridges: A:N.19

1 x K: POTASSIUM ION(Non-functional Binders)

K.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rolando, M. et al., The SET and ankyrin domains of the secreted Legionella pneumophila histone methyltransferase work together to modify host chromatin. Mbio (2023)

Release Date

2024-03-13

Peptides

Eukaryotic huntingtin interacting protein B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Eukaryotic huntingtin interacting protein B

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