SMTL ID : 7c4c.1

The crystal structure of Trypanosoma brucei RNase D : GMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.281, C.284, H.289, C.294 Ligands: 5GP.14 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.281, A:C.284, A:H.289, A:C.294 ZN.2: 4 residues within 4Å: Chain A: C.258, C.261, H.266, C.271 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.258, A:C.261, A:H.266, A:C.271 ZN.3: 3 residues within 4Å: Chain A: H.22, K.26, D.86 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.22, A:D.86, A:D.86 ZN.4: 2 residues within 4Å: Chain A: E.158, H.194 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.158, A:H.194, H2O.2 ZN.5: 4 residues within 4Å: Chain A: C.323, C.326, H.330, C.335 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.323, A:C.326, A:H.330, A:C.335 ZN.6: 4 residues within 4Å: Chain A: C.304, C.307, H.312, C.317 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.304, A:C.307, A:H.312, A:C.317

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.7: 5 residues within 4Å: Chain A: D.41, E.43, D.191 Ligands: MN.8, 5GP.13 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.41, A:E.43, A:D.191, H2O.1, 5GP.13 MN.8: 4 residues within 4Å: Chain A: D.41, D.106 Ligands: MN.7, 5GP.13 4 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.41, H2O.1, H2O.1, 5GP.13 MN.9: 3 residues within 4Å: Chain A: E.286, K.296 Ligands: 5GP.14 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.286, A:E.286 MN.10: 3 residues within 4Å: Chain A: Q.164, M.167 Ligands: 5GP.13 No protein-ligand interaction detected (PLIP) MN.11: 4 residues within 4Å: Chain A: A.291, R.292, K.297, H.298 No protein-ligand interaction detected (PLIP) MN.12: 1 residues within 4Å: Ligands: 5GP.16 No protein-ligand interaction detected (PLIP)

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

5GP.13: 13 residues within 4Å: Chain A: D.41, I.42, E.43, A.44, F.45, C.46, L.54, M.167, W.175, D.191 Ligands: MN.7, MN.8, MN.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.42, A:A.44, A:A.44 Water bridges: A:D.41, A:I.42, A:D.106 5GP.14: 7 residues within 4Å: Chain A: E.286, H.289, N.293, C.294, F.295 Ligands: ZN.1, MN.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.293, A:F.295 pi-Stacking: A:H.289, A:F.295 pi-Cation interactions: A:F.295 5GP.15: 7 residues within 4Å: Chain A: D.102, R.104, R.105, Q.125, R.141, G.143, P.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.102, A:R.104, A:Q.125 Water bridges: A:R.105 5GP.16: 5 residues within 4Å: Chain A: H.266, E.270, C.271, F.272 Ligands: MN.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.266, A:E.270, A:F.272 pi-Stacking: A:F.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei. Nucleic Acids Res. (2021)

Release Date

2021-04-07

Peptides

CCHC-type domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CCHC-type domain-containing protein

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