SMTL ID : 8ptx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain C: C.99, H.101, I.108, C.109, C.112, Q.125, R.223, R.260 Ligands: MET.4 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain C Metal complexes: MET.4, C:C.99, C:C.109, C:C.112

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

5AD.2: 10 residues within 4Å: Chain C: Y.111, P.113, Q.248, H.284, M.286, Y.318, P.319, L.321, R.367 Ligands: MET.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.248, C:L.321, C:L.321

1 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 23 residues within 4Å: Chain C: G.86, I.87, K.164, 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.87, C:T.526, C:Y.529, C:Y.530 Hydrogen bonds: C:K.164, C:V.477, C:S.485, C:Q.493, C:G.496, C:F.497, C:G.498, C:M.499, C:G.525, C:Y.529 Salt bridges: C:R.487

1 x MET: METHIONINE(Non-covalent)

MET.4: 10 residues within 4Å: Chain C: S.126, G.171, T.173, E.221, T.222, R.223, G.246, R.260 Ligands: SF4.1, 5AD.2 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.221 Hydrogen bonds: C:T.173, C:T.222, C:G.246 Salt bridges: C:R.260

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 1 residues within 4Å: Chain E: A.37 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain E: U.8, G.9, G.12 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain E: A.14 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain E: A.15, A.58 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: AD
Elongator complex protein 2: B
Elongator complex protein 3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

Elongator complex protein 1

Elongator complex protein 2

Elongator complex protein 3

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