SMTL ID : 8orj.1

Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: C.125, H.262, H.356 Chain B: D.502 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.125, A:H.262, A:H.356 MG.2: 5 residues within 4Å: Chain A: D.122, C.125, H.230 Chain B: D.502 Ligands: MG.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.122, A:C.125, A:H.230, B:D.502, B:D.502

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 19 residues within 4Å: Chain B: K.121, I.155, N.157, G.158, G.159, I.160, D.179, F.186, E.264, A.318, T.319, G.320, V.321, R.376, L.377, H.412, T.414, F.416 Ligands: FDA.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.160 Hydrogen bonds: B:K.121, B:N.157, B:N.157, B:N.157, B:G.159, B:I.160, B:D.179, B:E.264, B:G.320, B:T.414, B:T.414

1 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.4: 36 residues within 4Å: Chain B: V.18, G.19, G.20, G.21, I.22, A.23, V.43, T.44, A.45, G.88, V.89, C.115, A.116, G.117, A.118, I.133, R.134, I.160, E.163, G.234, S.235, A.236, L.237, G.238, P.239, W.241, N.324, P.327, D.360, R.376, L.377, W.378, A.381, H.412, T.414 Ligands: NAD.3 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.133, B:W.241 Hydrogen bonds: B:G.20, B:I.22, B:A.23, B:T.44, B:T.44, B:A.45, B:V.89, B:V.89, B:A.118, B:A.236, B:G.238, B:N.324, B:D.360, B:D.360, B:D.360, B:W.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loeff, L. et al., Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation. Nat.Struct.Mol.Biol. (2025)

Release Date

2024-10-30

Peptides

RNA-splicing ligase RtcB homolog: A
Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-splicing ligase RtcB homolog

Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1