SMTL ID : 8ptz.1

Cryo-EM structure of human Elp123 in complex with tRNA, S-ethyl-CoA, 5'-deoxyadenosine and methionine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain C: C.99, H.101, I.108, C.109, Y.111, C.112, Q.125, S.126, R.223, R.260 Ligands: MET.4 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.99, C:C.109, C:C.112

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 13 residues within 4Å: Chain C: Y.111, P.113, S.126, Y.127, Q.248, H.284, M.286, Y.318, P.319, L.321, I.323, R.367 Ligands: MET.4 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.127 Hydrogen bonds: C:Y.111, C:Q.248, C:H.284, C:L.321, M.4

1 x A2U: S-Ethyl-CoA

A2U.3: 24 residues within 4Å: Chain C: I.87, K.164, K.214, I.216, L.475, H.476, V.477, V.484, S.485, R.487, Q.493, H.494, Q.495, G.496, F.497, G.498, M.499, I.521, S.522, G.525, T.526, Y.529, Y.530, K.532 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.475, C:V.477, C:Y.529 Hydrogen bonds: C:K.164, C:S.485, C:G.496, C:F.497, C:G.498, C:G.525, C:Y.529 Salt bridges: C:R.487, C:K.532

1 x MET: METHIONINE(Non-covalent)

MET.4: 9 residues within 4Å: Chain C: G.171, G.172, E.221, T.222, R.223, G.246, R.260 Ligands: SF4.1, 5AD.2 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:E.221 Hydrogen bonds: C:G.172, C:G.246, M.4, M.4 Salt bridges: C:R.260

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 3 residues within 4Å: Chain C: K.79 Chain D: G.36, A.37 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain D: G.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abbassi, N.E. et al., Cryo-EM structures of the human Elongator complex at work. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Elongator complex protein 1: A
Elongator complex protein 2: B
Elongator complex protein 3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Elongator complex protein 1

Elongator complex protein 2

Elongator complex protein 3

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