SMTL ID : 7p3b.1 (1 other biounit)

Human RNA ligase RTCB in complex with GMP and Co(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 21 residues within 4Å: Chain A: I.98, C.124, 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: CO.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.228, A:Y.230, A:G.405, A:S.411, A:S.411, A:A.432, A:G.433, A:K.506 Water bridges: A:Q.234, A:N.356, A:G.404, A:M.407, A:M.407, A:H.430, A:H.430, A:Y.477 Salt bridges: A:E.232, A:H.261, A:H.355, A:H.430 pi-Stacking: A:Y.230 pi-Cation interactions: A:Y.230

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 5 residues within 4Å: Chain A: C.124, H.261, H.355 Ligands: 5GP.1, CO.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.124, A:H.261, A:H.355, 5GP.1 CO.3: 4 residues within 4Å: Chain A: D.121, C.124, H.229 Ligands: CO.2 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.121, A:C.124, A:H.229, H2O.3, H2O.3, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroupova, A. et al., Molecular architecture of the human tRNA ligase complex. Elife (2021)

Release Date

2021-12-22

Peptides

RNA-splicing ligase RtcB homolog: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-splicing ligase RtcB homolog

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