SMTL ID : 7onu.1

Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-1-mer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.17, A.19, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, I.94, V.120, T.153, A.154, S.155, Y.168, K.172, P.198, G.199, F.201, T.203, P.204, L.205, L.206 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.198 Hydrogen bonds: A:A.19, A:S.20, A:S.20, A:L.22, A:D.41, A:L.42, A:S.45, A:S.45, A:D.64, A:V.65, A:A.92, A:K.172, A:F.201, A:F.201, A:L.205 NAD.2: 27 residues within 4Å: Chain B: G.17, A.19, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, T.66, C.91, A.92, G.93, I.94, V.120, T.153, S.155, Y.168, K.172, P.198, G.199, F.201, T.203, P.204, L.205 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.198 Hydrogen bonds: B:A.19, B:S.20, B:S.20, B:S.20, B:L.22, B:L.42, B:D.64, B:D.64, B:V.65, B:T.66, B:A.92, B:Y.168, B:K.172, B:F.201, B:F.201, B:T.203 NAD.3: 25 residues within 4Å: Chain C: G.17, A.19, S.20, G.21, L.22, D.41, L.42, S.45, D.64, V.65, C.91, A.92, G.93, I.94, V.120, T.153, A.154, S.155, Y.168, K.172, G.199, F.201, T.203, P.204, L.205 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.17, C:A.19, C:S.20, C:S.20, C:L.22, C:D.41, C:L.42, C:D.64, C:V.65, C:C.91, C:F.201, C:F.201 NAD.4: 27 residues within 4Å: Chain D: G.17, A.19, S.20, G.21, L.22, D.41, L.42, S.45, A.63, D.64, V.65, C.91, A.92, G.93, I.94, V.120, T.153, A.154, S.155, Y.168, K.172, P.198, F.201, T.203, P.204, L.205, L.206 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:A.19, D:S.20, D:S.20, D:S.20, D:S.20, D:L.22, D:L.42, D:D.64, D:V.65, D:T.66, D:A.92, D:G.93, D:Y.168, D:K.172, D:F.201, D:F.201, D:T.203, D:L.205

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain E: C.306, C.309, H.515, C.536, H.538 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.306, E:C.309, E:H.515, E:C.536

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain E: D.437, D.457, D.461, H.462 Chain G: G.39 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.437, E:D.457

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhatta, A. et al., Structural basis of RNA processing by human mitochondrial RNase P. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-08-11

Peptides

3-hydroxyacyl-CoA dehydrogenase type-2: ABCD
Mitochondrial ribonuclease P catalytic subunit: E
tRNA methyltransferase 10 homolog C: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

3-hydroxyacyl-CoA dehydrogenase type-2

Mitochondrial ribonuclease P catalytic subunit

tRNA methyltransferase 10 homolog C

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