SMTL ID : 8odo.1 (3 other biounits)

Structure of human guanylylated RTCB in complex with Archease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Covalent)

5GP.1: 20 residues within 4Å: Chain A: I.98, N.228, Y.230, E.232, Q.234, H.261, H.355, G.404, G.405, T.406, M.407, S.411, H.430, G.431, A.432, G.433, Y.477, V.504, K.506 Ligands: MN.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.228, A:Q.234, A:G.405, A:S.411, A:S.411, A:A.432, A:G.433, A:E.472, A:K.506 Water bridges: A:N.356, A:M.407, A:M.407 Salt bridges: A:E.232, A:H.261, A:H.355, A:H.430 pi-Stacking: A:Y.230, A:Y.477 pi-Cation interactions: A:Y.230

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: C.124, H.261, H.355 Ligands: 5GP.1 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:C.124, A:H.261, A:H.355, 5GP.1, H2O.2 MN.4: 4 residues within 4Å: Chain B: D.72, D.199, I.200 Ligands: PO4.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.199, B:I.200, H2O.8, H2O.8

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: Y.94, D.121, N.356, K.377 Chain B: K.177, D.199, I.200 Ligands: MN.4 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Water bridges: B:K.177, A:D.121, A:N.228, A:N.228, A:N.356, A:K.377 Salt bridges: B:K.177, A:K.377 Hydrogen bonds: A:Y.94, A:D.121, A:N.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerber, J.L. et al., Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Nat Commun (2024)

Release Date

2024-03-27

Peptides

RNA-splicing ligase RtcB homolog: A
Protein archease: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-splicing ligase RtcB homolog

Protein archease

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