SMTL ID : 8odp.4 (3 other biounits)

Structure of human RTCB with GMPCPP in complex with Archease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.124, H.261, H.355 Ligands: MN.2, G2P.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.124, A:H.261, A:H.355, H2O.1 MN.2: 6 residues within 4Å: Chain A: D.121, C.124, H.229 Chain B: K.160 Ligands: MN.1, G2P.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.121, A:C.124, A:H.229 MN.4: 4 residues within 4Å: Chain B: D.55, D.182, I.183 Ligands: G2P.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.55, B:D.182, B:I.183, H2O.1, H2O.1

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.3: 28 residues within 4Å: Chain A: D.121, C.124, N.228, H.229, Y.230, E.232, Q.234, H.261, H.355, N.356, K.377, G.404, G.405, T.406, M.407, S.411, H.430, G.431, A.432, G.433, Y.477, K.506 Chain B: K.160, D.182, I.183 Ligands: MN.1, MN.2, MN.4 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.228, A:E.232, A:Q.234, A:N.356, A:G.405, A:G.405, A:S.411, A:S.411, A:A.432, A:G.433, B:K.160 Water bridges: A:R.438 Salt bridges: A:E.232, A:K.377, B:K.160 pi-Stacking: A:Y.230, A:Y.477 pi-Cation interactions: A:Y.230

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
G

B
H

RNA-splicing ligase RtcB homolog

Protein archease

Related Entries With Identical Sequence